Preparation and analysis of data: Tang et al, AJP, Image-based machine learning algorithms for disease characterization in the human type 1 diabetes pancreas

Dependencies

This notebook uses SAS and R. R is free, SAS is not. You must have a SAS license to run SAS or use SAS University Edition. See our github page from a previous publication that describes the installation process of SAS University Edition.

In addition, you need to install the SAS kernal for jupyter notebook, available here: https://github.com/sassoftware/sas_kernel

All file paths in this notebook will need to be revised to the destination you choose to place this notebook and all the datafiles.

r packages and set the working directory consider use of packrat to save R packages and versions locally with each project (improve reproducibility)

In [87]:
#install.packages(c("ggthemes", "ggpubr"))
In [88]:
#.libPaths()
In [89]:
#to see color code for brewer palette for donorgroups
#brewer.pal(8, "Dark2")

#to see color code for brewer palette for pancreas head, body, tail
#brewer.pal(11, "BrBG")

The below libraries are needed. Issues related to library installation may be related to set up and machine, therefore not addressed here. Make sure all packages are installed prior to loading, i.e. install.packages

In [90]:
library(ggplot2)
library(beeswarm)
library(ggbeeswarm)
library(rio)
library(tidyverse)
library(magrittr)
library(ggthemes)
library(plyr)
library(dplyr)
library(readr)
library(cowplot)
library(ggpubr)
library(RColorBrewer)
library(ggsignif)
library(shadowtext)


#for use when connected to network
#setwd('F://Manuscripts//nPOD_requests//pancreas_size//data')

#for use when off network
setwd('C://Users//jkaddis//Desktop//pancreas_size//data')

setting location of data files for use in SAS

In [91]:
%let location= C:\Users\jkaddis\Desktop\pancreas_size;

*%let location= F:\Manuscripts\nPOD_requests\pancreas_size;
Out[91]:

58                                                         The SAS System                         22:22 Wednesday, November 11, 2020

9051 ods listing close;ods html5 (id=saspy_internal) file=_tomods1 options(bitmap_mode='inline') device=svg style=HTMLBlue;
9051 ! ods graphics on / outputfmt=png;
NOTE: Writing HTML5(SASPY_INTERNAL) Body file: _TOMODS1
9052
9053 %let location= C:\Users\jkaddis\Desktop\pancreas_size;
9054
9055 *%let location= F:\Manuscripts\nPOD_requests\pancreas_size;
9056
9057
9058 ods html5 (id=saspy_internal) close;ods listing;
9059

basic data prep work

Medical and clinical datasets downloaded from datashare. Latest download of data on July 7, 2019.

In [92]:
PROC import datafile = "&location\Data\Demographics_2019-07-09_17-12-02.xlsx" 
     out      = demographics 
     dbms = xlsx replace;
     getnames=yes;
RUN;

PROC import datafile = "&location\Data\Pancreas Weights_2019-07-09_17-12-46.xlsx" 
     out      = panc_weights 
     dbms = xlsx replace;
     getnames=yes;
RUN;

PROC import datafile = "&location\Data\Duration of Donor Hospitalization_2019-07-09_17-13-07.xlsx" 
     out      = hosp_time 
     dbms = xlsx replace;
     getnames=yes;
RUN;

PROC import datafile = "&location\Data\Organ Transportation Time_2019-07-09_17-13-20.xlsx" 
     out      = transport_time 
     dbms = xlsx replace;
     getnames=yes;
RUN;

PROC import datafile = "&location\Data\RIA_AutoAb_Results_2019-07-10_05-18-45.xlsx" 
     out      = antibodies 
     dbms = xlsx replace;
     getnames=yes;
RUN;


PROC import datafile = "&location\Data\Hi Res HLA Post Receipt of Organ_2019-07-29_15-25-54.xlsx" 
     out      = HLA 
     dbms = xlsx replace;
     getnames=yes;
RUN;

DATA HLA;
    set HLA;
    rename 'nPOD CaseID'n=nPODCaseID;
RUN;
Out[92]:

59                                                         The SAS System                         22:22 Wednesday, November 11, 2020

9062 ods listing close;ods html5 (id=saspy_internal) file=_tomods1 options(bitmap_mode='inline') device=svg style=HTMLBlue;
9062 ! ods graphics on / outputfmt=png;
NOTE: Writing HTML5(SASPY_INTERNAL) Body file: _TOMODS1
9063
9064 PROC import datafile = "&location\Data\Demographics_2019-07-09_17-12-02.xlsx"
9065 out = demographics
9066 dbms = xlsx replace;
9067 getnames=yes;
9068 RUN;

NOTE: The import data set has 551 observations and 11 variables.
NOTE: WORK.DEMOGRAPHICS data set was successfully created.
NOTE: PROCEDURE IMPORT used (Total process time):
real time 0.05 seconds
cpu time 0.04 seconds


9069
9070 PROC import datafile = "&location\Data\Pancreas Weights_2019-07-09_17-12-46.xlsx"
9071 out = panc_weights
9072 dbms = xlsx replace;
9073 getnames=yes;
9074 RUN;

NOTE: The import data set has 552 observations and 8 variables.
NOTE: WORK.PANC_WEIGHTS data set was successfully created.
NOTE: PROCEDURE IMPORT used (Total process time):
real time 0.03 seconds
cpu time 0.04 seconds


9075
9076 PROC import datafile = "&location\Data\Duration of Donor Hospitalization_2019-07-09_17-13-07.xlsx"
9077 out = hosp_time
9078 dbms = xlsx replace;
9079 getnames=yes;
9080 RUN;

NOTE: The import data set has 554 observations and 4 variables.
NOTE: WORK.HOSP_TIME data set was successfully created.
NOTE: PROCEDURE IMPORT used (Total process time):
real time 0.02 seconds
cpu time 0.03 seconds


9081
9082 PROC import datafile = "&location\Data\Organ Transportation Time_2019-07-09_17-13-20.xlsx"
9083 out = transport_time
9084 dbms = xlsx replace;
9085 getnames=yes;
9086 RUN;

NOTE: The import data set has 554 observations and 4 variables.
NOTE: WORK.TRANSPORT_TIME data set was successfully created.
NOTE: PROCEDURE IMPORT used (Total process time):
real time 0.03 seconds
cpu time 0.03 seconds


9087
9088 PROC import datafile = "&location\Data\RIA_AutoAb_Results_2019-07-10_05-18-45.xlsx"
9089 out = antibodies
9090 dbms = xlsx replace;
9091 getnames=yes;
9092 RUN;

NOTE: The import data set has 545 observations and 10 variables.
NOTE: WORK.ANTIBODIES data set was successfully created.
NOTE: PROCEDURE IMPORT used (Total process time):
real time 0.07 seconds
cpu time 0.07 seconds


9093
9094
9095 PROC import datafile = "&location\Data\Hi Res HLA Post Receipt of Organ_2019-07-29_15-25-54.xlsx"
9096 out = HLA
9097 dbms = xlsx replace;
9098 getnames=yes;
9099 RUN;

NOTE: The import data set has 556 observations and 26 variables.
NOTE: WORK.HLA data set was successfully created.
NOTE: PROCEDURE IMPORT used (Total process time):
real time 0.09 seconds
cpu time 0.09 seconds


9100
9101 DATA HLA;
9102 set HLA;
9103 rename 'nPOD CaseID'n=nPODCaseID;
9104 RUN;

NOTE: There were 556 observations read from the data set WORK.HLA.
NOTE: The data set WORK.HLA has 556 observations and 26 variables.
NOTE: DATA statement used (Total process time):
real time 0.01 seconds
cpu time 0.01 seconds


9105
9106
9107 ods html5 (id=saspy_internal) close;ods listing;
9108

The diabetes dataset has text fields with line breaks, which corrupts the file import. Below code solves that problem and was adpoted from http://support.sas.com/kb/26/065.html

In [93]:
/************************** CAUTION ***************************/
/*                                                            */
/* This program UPDATES IN PLACE, create a backup copy before */
/* running.                                                   */
/*                                                            */
/************************** CAUTION ***************************/
                                                           
/* Replace carriage return and linefeed characters inside     */
/* double quotes with a specified character.  This sample     */
/* uses '@' and '$', but any character can be used, including */
/* spaces.  CR/LFs not in double quotes will not be replaced. */


%let repA='@';                    /* replacement character LF */
%let repD='$';                    /* replacement character CR */

                             
%let dsnnme="&location\Data\Diabetes Information_2019-07-09_17-13-50.csv";      /* use full path of CSV file */

data _null_;
  /* RECFM=N reads the file in binary format. The file consists    */
  /* of a stream of bytes with no record boundaries.  SHAREBUFFERS */
  /* specifies that the FILE statement and the INFILE statement    */
  /* share the same buffer.                                        */
  infile &dsnnme recfm=n sharebuffers;
  file &dsnnme recfm=n;

  /* OPEN is a flag variable used to determine if the CR/LF is within */
  /* double quotes or not.  Retain this value.                        */
  retain open 0;

  input a $char1.;
  /* If the character is a double quote, set OPEN to its opposite value. */
  if a = '"' then open = ^(open);

  /* If the CR or LF is after an open double quote, replace the byte with */
  /* the appropriate value.                                               */
  if open then do;
    if a = '0D'x then put &repD;
    else if a = '0A'x then put &repA;
  end;
run;

PROC import datafile = "&location\Data\Diabetes Information_2019-07-09_17-13-50.csv" 
     out      = diabetes 
     dbms = csv replace;
     getnames=yes;
     guessingrows=1000;
RUN;
Out[93]:

60                                                         The SAS System                         22:22 Wednesday, November 11, 2020

9111 ods listing close;ods html5 (id=saspy_internal) file=_tomods1 options(bitmap_mode='inline') device=svg style=HTMLBlue;
9111 ! ods graphics on / outputfmt=png;
NOTE: Writing HTML5(SASPY_INTERNAL) Body file: _TOMODS1
9112
9113 /************************** CAUTION ***************************/
9114 /* */
9115 /* This program UPDATES IN PLACE, create a backup copy before */
9116 /* running. */
9117 /* */
9118 /************************** CAUTION ***************************/
9119
9120 /* Replace carriage return and linefeed characters inside */
9121 /* double quotes with a specified character. This sample */
9122 /* uses '@' and '$', but any character can be used, including */
9123 /* spaces. CR/LFs not in double quotes will not be replaced. */
9124
9125
9126 %let repA='@'; /* replacement character LF */
9127 %let repD='$'; /* replacement character CR */
9128
9129
9130 %let dsnnme="&location\Data\Diabetes Information_2019-07-09_17-13-50.csv"; /* use full path of CSV file */
9131
9132 data _null_;
9133 /* RECFM=N reads the file in binary format. The file consists */
9134 /* of a stream of bytes with no record boundaries. SHAREBUFFERS */
9135 /* specifies that the FILE statement and the INFILE statement */
9136 /* share the same buffer. */
9137 infile &dsnnme recfm=n sharebuffers;
9138 file &dsnnme recfm=n;
9139
9140 /* OPEN is a flag variable used to determine if the CR/LF is within */
9141 /* double quotes or not. Retain this value. */
9142 retain open 0;
9143
9144 input a $char1.;
9145 /* If the character is a double quote, set OPEN to its opposite value. */
9146 if a = '"' then open = ^(open);
9147
9148 /* If the CR or LF is after an open double quote, replace the byte with */
9149 /* the appropriate value. */
9150 if open then do;
9151 if a = '0D'x then put &repD;
9152 else if a = '0A'x then put &repA;
9153 end;
9154 run;

NOTE: UNBUFFERED is the default with RECFM=N.
NOTE: The file/infile "C:\Users\jkaddis\Desktop\pancreas_size\Data\Diabetes Information_2019-07-09_17-13-50.csv" is:
Filename=C:\Users\jkaddis\Desktop\pancreas_size\Data\Diabetes Information_2019-07-09_17-13-50.csv,
RECFM=N,LRECL=256,File Size (bytes)=32630,
Last Modified=09Jul2019:17:17:29,
Create Time=11Nov2020:22:21:04

NOTE: UNBUFFERED is the default with RECFM=N.
NOTE: DATA statement used (Total process time):
real time 0.18 seconds
cpu time 0.18 seconds


9155
9156 PROC import datafile = "&location\Data\Diabetes Information_2019-07-09_17-13-50.csv"
9157 out = diabetes
9158 dbms = csv replace;
9159 getnames=yes;
9160 guessingrows=1000;
9161 RUN;

9162 /**********************************************************************
9163 * PRODUCT: SAS
9164 * VERSION: 9.4
9165 * CREATOR: External File Interface
9166 * DATE: 11NOV20
9167 * DESC: Generated SAS Datastep Code
9168 * TEMPLATE SOURCE: (None Specified.)
9169 ***********************************************************************/
9170 data WORK.DIABETES ;
9171 %let _EFIERR_ = 0; /* set the ERROR detection macro variable */
9172 infile 'C:\Users\jkaddis\Desktop\pancreas_size\Data\Diabetes Information_2019-07-09_17-13-50.csv' delimiter = ','
9172 ! MISSOVER DSD lrecl=32767 firstobs=2 ;
9173 informat nPODCaseID $8. ;
9174 informat "DataSets/Demographics/DonorType"N $24. ;
9175 informat diabetes_Duration_yrs best32. ;
9176 informat oppc_C_peptideR $14. ;
9177 informat oppc_HbA1cR best32. ;
9178 informat diabetes_history $20. ;
9179 informat Insulin_depd $20. ;
9180 informat Insulin_meds_taken $169. ;
9181 format nPODCaseID $8. ;
9182 format "DataSets/Demographics/DonorType"N $24. ;
9183 format diabetes_Duration_yrs best12. ;
9184 format oppc_C_peptideR $14. ;
9185 format oppc_HbA1cR best12. ;
9186 format diabetes_history $20. ;
9187 format Insulin_depd $20. ;
9188 format Insulin_meds_taken $169. ;
9189 input
9190 nPODCaseID $
9191 "DataSets/Demographics/DonorType"N $
9192 diabetes_Duration_yrs
9193 oppc_C_peptideR $
9194 oppc_HbA1cR
9195 diabetes_history $
9196 Insulin_depd $
9197 Insulin_meds_taken $
9198 ;
9199 if _ERROR_ then call symputx('_EFIERR_',1); /* set ERROR detection macro variable */
9200 run;

NOTE: The infile 'C:\Users\jkaddis\Desktop\pancreas_size\Data\Diabetes Information_2019-07-09_17-13-50.csv' is:
Filename=C:\Users\jkaddis\Desktop\pancreas_size\Data\Diabetes Information_2019-07-09_17-13-50.csv,
RECFM=V,LRECL=32767,File Size (bytes)=32630,
Last Modified=09Jul2019:17:17:29,
Create Time=11Nov2020:22:21:04

NOTE: 551 records were read from the infile 'C:\Users\jkaddis\Desktop\pancreas_size\Data\Diabetes
Information_2019-07-09_17-13-50.csv'.
The minimum record length was 10.
The maximum record length was 225.
NOTE: The data set WORK.DIABETES has 551 observations and 8 variables.
NOTE: DATA statement used (Total process time):
real time 0.01 seconds
cpu time 0.01 seconds


551 rows created in WORK.DIABETES from C:\Users\jkaddis\Desktop\pancreas_size\Data\Diabetes Information_2019-07-09_17-13-50.csv.



NOTE: WORK.DIABETES data set was successfully created.
NOTE: The data set WORK.DIABETES has 551 observations and 8 variables.
NOTE: PROCEDURE IMPORT used (Total process time):
real time 0.13 seconds
cpu time 0.14 seconds


9201
9202
9203 ods html5 (id=saspy_internal) close;ods listing;
9204

Merge all datasets

In [94]:
/*due to jupyter notebook magics, this line of code is needed when creating a new macro.  As long as there is a 
line before the %macro, the cell will be interpretted correctly.  This is not needed if running SAS natively*/

%macro sort (D);
PROC sort data=&D;
by nPODCaseID;
RUN;
%mend sort;

%sort (demographics); run;
%sort (diabetes); run;
%sort (panc_weights); run;
%sort (hosp_time); run;
%sort (transport_time); run;
%sort (antibodies); run;
%sort (HLA); run;

DATA clinical;
    merge demographics diabetes panc_weights hosp_time transport_time antibodies HLA;
    by nPODCaseID;
RUN;

/*inspect dataset outside of notebook*/
PROC export data=clinical 
     outfile="&location\Data\clinical.csv" 
     dbms=csv
     replace;
run;
Out[94]:

61                                                         The SAS System                         22:22 Wednesday, November 11, 2020

9207 ods listing close;ods html5 (id=saspy_internal) file=_tomods1 options(bitmap_mode='inline') device=svg style=HTMLBlue;
9207 ! ods graphics on / outputfmt=png;
NOTE: Writing HTML5(SASPY_INTERNAL) Body file: _TOMODS1
9208
9209 /*due to jupyter notebook magics, this line of code is needed when creating a new macro. As long as there is a
9210 line before the %macro, the cell will be interpretted correctly. This is not needed if running SAS natively*/
9211
9212 %macro sort (D);
9213 PROC sort data=&D;
9214 by nPODCaseID;
9215 RUN;
9216 %mend sort;
9217
9218 %sort (demographics); run;

NOTE: There were 551 observations read from the data set WORK.DEMOGRAPHICS.
NOTE: The data set WORK.DEMOGRAPHICS has 551 observations and 11 variables.
NOTE: PROCEDURE SORT used (Total process time):
real time 0.00 seconds
cpu time 0.01 seconds


9219 %sort (diabetes); run;

NOTE: There were 551 observations read from the data set WORK.DIABETES.
NOTE: The data set WORK.DIABETES has 551 observations and 8 variables.
NOTE: PROCEDURE SORT used (Total process time):
real time 0.00 seconds
cpu time 0.00 seconds


9220 %sort (panc_weights); run;

NOTE: There were 552 observations read from the data set WORK.PANC_WEIGHTS.
NOTE: The data set WORK.PANC_WEIGHTS has 552 observations and 8 variables.
NOTE: PROCEDURE SORT used (Total process time):
real time 0.00 seconds
cpu time 0.00 seconds


9221 %sort (hosp_time); run;

NOTE: There were 554 observations read from the data set WORK.HOSP_TIME.
NOTE: The data set WORK.HOSP_TIME has 554 observations and 4 variables.
NOTE: PROCEDURE SORT used (Total process time):
real time 0.00 seconds
cpu time 0.00 seconds


9222 %sort (transport_time); run;

NOTE: There were 554 observations read from the data set WORK.TRANSPORT_TIME.
NOTE: The data set WORK.TRANSPORT_TIME has 554 observations and 4 variables.
NOTE: PROCEDURE SORT used (Total process time):
real time 0.00 seconds
cpu time 0.01 seconds


9223 %sort (antibodies); run;

NOTE: There were 545 observations read from the data set WORK.ANTIBODIES.
NOTE: The data set WORK.ANTIBODIES has 545 observations and 10 variables.
NOTE: PROCEDURE SORT used (Total process time):
real time 0.00 seconds
cpu time 0.00 seconds


9224 %sort (HLA); run;

NOTE: There were 556 observations read from the data set WORK.HLA.
NOTE: The data set WORK.HLA has 556 observations and 26 variables.
NOTE: PROCEDURE SORT used (Total process time):
real time 0.00 seconds
cpu time 0.00 seconds


9225
9226 DATA clinical;
9227 merge demographics diabetes panc_weights hosp_time transport_time antibodies HLA;
9228 by nPODCaseID;
9229 RUN;

NOTE: There were 551 observations read from the data set WORK.DEMOGRAPHICS.
NOTE: There were 551 observations read from the data set WORK.DIABETES.
NOTE: There were 552 observations read from the data set WORK.PANC_WEIGHTS.
NOTE: There were 554 observations read from the data set WORK.HOSP_TIME.
NOTE: There were 554 observations read from the data set WORK.TRANSPORT_TIME.
NOTE: There were 545 observations read from the data set WORK.ANTIBODIES.
NOTE: There were 556 observations read from the data set WORK.HLA.
NOTE: The data set WORK.CLINICAL has 560 observations and 61 variables.
NOTE: DATA statement used (Total process time):
real time 0.02 seconds
cpu time 0.03 seconds


9230
9231 /*inspect dataset outside of notebook*/
9232 PROC export data=clinical
9233 outfile="&location\Data\clinical.csv"
9234 dbms=csv
9235 replace;
9236 run;

9237 /**********************************************************************
9238 * PRODUCT: SAS
9239 * VERSION: 9.4
9240 * CREATOR: External File Interface
9241 * DATE: 11NOV20
9242 * DESC: Generated SAS Datastep Code
9243 * TEMPLATE SOURCE: (None Specified.)
9244 ***********************************************************************/
9245 data _null_;
9246 %let _EFIERR_ = 0; /* set the ERROR detection macro variable */
9247 %let _EFIREC_ = 0; /* clear export record count macro variable */
9248 file 'C:\Users\jkaddis\Desktop\pancreas_size\Data\clinical.csv' delimiter=',' DSD DROPOVER lrecl=32767;
9249 if _n_ = 1 then /* write column names or labels */
9250 do;
9251 put
9252 "nPODCaseID"
9253 ','
9254 "DonorType"
9255 ','
9256 "oppc_ageR"
9257 ','
9258 "oppc_Gender"
9259 ','
9260 "oppc_Ethnicity"
9261 ','
9262 "oppc_heightR"
9263 ','
9264 "oppc_weightR"
9265 ','
9266 "oppc_bmiR"
9267 ','
9268 "oppc_abo"
9269 ','
9270 "abo_subtype"
9271 ','
9272 "cod_final"
9273 ','
9274 "DataSets/Demographics/DonorType"
9275 ','
9276 "diabetes_Duration_yrs"
9277 ','
9278 "oppc_C_peptideR"
9279 ','
9280 "oppc_HbA1cR"
9281 ','
9282 "diabetes_history"
9283 ','
9284 "Insulin_depd"
9285 ','
9286 "Insulin_meds_taken"
9287 ','
9288 "Pancreas_Received_Intact"
9289 ','
9290 "whole_pancreas_g"
9291 ','
9292 "panhead_g"
9293 ','
9294 "panbody_g"
9295 ','
9296 "pantail_g"
9297 ','
9298 "Comments"
9299 ','
9300 "hospitalization_stay_minutes"
9301 ','
9302 "hospitalization_stay_days"
9303 ','
9304 "transport_duration_minutes"
9305 ','
9306 "transport_duration_hours"
9307 ','
9308 "date"
9309 ','
9310 "GADA_Result"
9311 ','
9312 "IA_2A_Result"
9313 ','
9314 "mIAA_Result"
9315 ','
9316 "Znt8A_Result"
9317 ','
9318 "Total_Positive_AutoAb_Count"
9319 ','
9320 "Sample"
9321 ','
9322 "Public_Comments"
9323 ','
9324 "Donor Type"
9325 ','
9326 "Transplant(A_1)"
9327 ','
9328 "Transplant(A_2)"
9329 ','
9330 "Transplant(B_1)"
9331 ','
9332 "Transplant(B_2)"
9333 ','
9334 "Transplant(DR_1)"
9335 ','
9336 "Transplant(DR_2)"
9337 ','
9338 "Transplant(DQ_1)"
9339 ','
9340 "Transplant(DQ_2)"
9341 ','
9342 "A_1"
9343 ','
9344 "A_2"
9345 ','
9346 "B_1"
9347 ','
9348 "B_2"
9349 ','
9350 "C_1"
9351 ','
9352 "C_2"
9353 ','
9354 "DRB1_1"
9355 ','
9356 "DRB1_2"
9357 ','
9358 "DQA1_1"
9359 ','
9360 "DQA1_2"
9361 ','
9362 "DQB1_1"
9363 ','
9364 "DQB1_2"
9365 ','
9366 "DPA1_1"
9367 ','
9368 "DPA1_2"
9369 ','
9370 "DPB1_1"
9371 ','
9372 "DPB1_2"
9373 ;
9374 end;
9375 set CLINICAL end=EFIEOD;
9376 format nPODCaseID $8. ;
9377 format DonorType $24. ;
9378 format oppc_ageR comma15.4 ;
9379 format oppc_Gender $6. ;
9380 format oppc_Ethnicity $29. ;
9381 format oppc_heightR comma15.4 ;
9382 format oppc_weightR comma15.4 ;
9383 format oppc_bmiR comma15.1 ;
9384 format oppc_abo $3. ;
9385 format abo_subtype $3. ;
9386 format cod_final $50. ;
9387 format "DataSets/Demographics/DonorType"N $24. ;
9388 format diabetes_Duration_yrs best12. ;
9389 format oppc_C_peptideR $14. ;
9390 format oppc_HbA1cR best12. ;
9391 format diabetes_history $20. ;
9392 format Insulin_depd $20. ;
9393 format Insulin_meds_taken $169. ;
9394 format Pancreas_Received_Intact $5. ;
9395 format whole_pancreas_g best12. ;
9396 format panhead_g best12. ;
9397 format panbody_g best12. ;
9398 format pantail_g best12. ;
9399 format Comments $134. ;
9400 format hospitalization_stay_minutes best12. ;
9401 format hospitalization_stay_days comma15.4 ;
9402 format transport_duration_minutes best12. ;
9403 format transport_duration_hours comma15.4 ;
9404 format date date9. ;
9405 format GADA_Result $10. ;
9406 format IA_2A_Result $10. ;
9407 format mIAA_Result $10. ;
9408 format Znt8A_Result $10. ;
9409 format Total_Positive_AutoAb_Count best12. ;
9410 format Sample $16. ;
9411 format Public_Comments $641. ;
9412 format "Donor Type"N $24. ;
9413 format "Transplant(A_1)"N $6. ;
9414 format "Transplant(A_2)"N $6. ;
9415 format "Transplant(B_1)"N $5. ;
9416 format "Transplant(B_2)"N $6. ;
9417 format "Transplant(DR_1)"N $6. ;
9418 format "Transplant(DR_2)"N $6. ;
9419 format "Transplant(DQ_1)"N $6. ;
9420 format "Transplant(DQ_2)"N $6. ;
9421 format A_1 $5. ;
9422 format A_2 $5. ;
9423 format B_1 $5. ;
9424 format B_2 $5. ;
9425 format C_1 $5. ;
9426 format C_2 $5. ;
9427 format DRB1_1 $8. ;
9428 format DRB1_2 $7. ;
9429 format DQA1_1 $7. ;
9430 format DQA1_2 $7. ;
9431 format DQB1_1 $7. ;
9432 format DQB1_2 $7. ;
9433 format DPA1_1 $5. ;
9434 format DPA1_2 $5. ;
9435 format DPB1_1 $5. ;
9436 format DPB1_2 $5. ;
9437 do;
9438 EFIOUT + 1;
9439 put nPODCaseID $ @;
9440 put DonorType $ @;
9441 put oppc_ageR @;
9442 put oppc_Gender $ @;
9443 put oppc_Ethnicity $ @;
9444 put oppc_heightR @;
9445 put oppc_weightR @;
9446 put oppc_bmiR @;
9447 put oppc_abo $ @;
9448 put abo_subtype $ @;
9449 put cod_final $ @;
9450 put "DataSets/Demographics/DonorType"N $ @;
9451 put diabetes_Duration_yrs @;
9452 put oppc_C_peptideR $ @;
9453 put oppc_HbA1cR @;
9454 put diabetes_history $ @;
9455 put Insulin_depd $ @;
9456 put Insulin_meds_taken $ @;
9457 put Pancreas_Received_Intact $ @;
9458 put whole_pancreas_g @;
9459 put panhead_g @;
9460 put panbody_g @;
9461 put pantail_g @;
9462 put Comments $ @;
9463 put hospitalization_stay_minutes @;
9464 put hospitalization_stay_days @;
9465 put transport_duration_minutes @;
9466 put transport_duration_hours @;
9467 put date @;
9468 put GADA_Result $ @;
9469 put IA_2A_Result $ @;
9470 put mIAA_Result $ @;
9471 put Znt8A_Result $ @;
9472 put Total_Positive_AutoAb_Count @;
9473 put Sample $ @;
9474 put Public_Comments $ @;
9475 put "Donor Type"N $ @;
9476 put "Transplant(A_1)"N $ @;
9477 put "Transplant(A_2)"N $ @;
9478 put "Transplant(B_1)"N $ @;
9479 put "Transplant(B_2)"N $ @;
9480 put "Transplant(DR_1)"N $ @;
9481 put "Transplant(DR_2)"N $ @;
9482 put "Transplant(DQ_1)"N $ @;
9483 put "Transplant(DQ_2)"N $ @;
9484 put A_1 $ @;
9485 put A_2 $ @;
9486 put B_1 $ @;
9487 put B_2 $ @;
9488 put C_1 $ @;
9489 put C_2 $ @;
9490 put DRB1_1 $ @;
9491 put DRB1_2 $ @;
9492 put DQA1_1 $ @;
9493 put DQA1_2 $ @;
9494 put DQB1_1 $ @;
9495 put DQB1_2 $ @;
9496 put DPA1_1 $ @;
9497 put DPA1_2 $ @;
9498 put DPB1_1 $ @;
9499 put DPB1_2 $ ;
9500 ;
9501 end;
9502 if _ERROR_ then call symputx('_EFIERR_',1); /* set ERROR detection macro variable */
9503 if EFIEOD then call symputx('_EFIREC_',EFIOUT);
9504 run;

NOTE: The file 'C:\Users\jkaddis\Desktop\pancreas_size\Data\clinical.csv' is:
Filename=C:\Users\jkaddis\Desktop\pancreas_size\Data\clinical.csv,
RECFM=V,LRECL=32767,File Size (bytes)=0,
Last Modified=12Nov2020:01:20:46,
Create Time=11Nov2020:22:23:24

NOTE: 561 records were written to the file 'C:\Users\jkaddis\Desktop\pancreas_size\Data\clinical.csv'.
The minimum record length was 64.
The maximum record length was 1077.
NOTE: There were 560 observations read from the data set WORK.CLINICAL.
NOTE: DATA statement used (Total process time):
real time 0.07 seconds
cpu time 0.07 seconds


560 records created in C:\Users\jkaddis\Desktop\pancreas_size\Data\clinical.csv from CLINICAL.


NOTE: "C:\Users\jkaddis\Desktop\pancreas_size\Data\clinical.csv" file was successfully created.
NOTE: PROCEDURE EXPORT used (Total process time):
real time 0.12 seconds
cpu time 0.12 seconds


9505
9506
9507 ods html5 (id=saspy_internal) close;ods listing;
9508

clean up clinical dataset for analysis

In [95]:
DATA clinical1;
    set clinical;
    
    oppc_ethnicity1=oppc_Ethnicity;
    if oppc_Ethnicity="American Indian/Alaska Native" then oppc_ethnicity1="Other";
    if oppc_Ethnicity="Asian" then oppc_ethnicity1="Other";
    if oppc_Ethnicity="Multiracial" then oppc_ethnicity1="Other";
    
    *donortype1=compress(donortype,'','s');
    donortype1=DonorType;
    if DonorType1="Cystic fibrosis" then donortype1="Other";
    if DonorType1="Gestational diabetes" then donortype1="Other";
    if DonorType1="Pending" then donortype1="Other";
    if DonorType1="Pregnancy" then donortype1="Other";
    
    cod4group=99;
    if cod_final="" then cod4group='.';
    IF cod_final="ANOXIA" then cod4group=1; /*anoxia*/
    IF cod_final="CEREBROVASCULAR/STROKE" then cod4group=2; /*cerebrovascular/stroke*/
    IF cod_final="Other: Cardiovascular" then cod4group=2; /*cerebrovascular/stroke*/
    IF cod_final="Cerebral edema" then cod4group=2; /*cerebrovascular/stroke*/
    IF cod_final="HEAD TRAUMA" then cod4group=3; /*head trauma*/
    if cod_final="Cystic Fibrosis" then cod4group=4; /*other*/
    if cod_final="DKA" then cod4group=4; /*other*/
    if cod_final="DKA, cerebral edema" then cod4group=4; /*other*/
    if cod_final="Cystic Fibrosis" then cod4group=4; /*other*/
    if cod_final="Cystic Fibrosis" then cod4group=4; /*other*/
    if cod_final="Cystic Fibrosis" then cod4group=4; /*other*/
    if cod_final="Infectious Disease - Bacterial Meningitis" then cod4group=4; /*other*/
    if cod_final="Meningitis" then cod4group=4; /*other*/
    if cod_final="Perinatal Condition/Birth Defect" then cod4group=4; /*other*/
    if cod_final="Respiratory Distress/Failure" then cod4group=4; /*other*/
    if cod_final="Spinal Cord Injury" then cod4group=4; /*other*/
    
    oppc_c_peptideR1=.;
    if oppc_c_peptideR="Less than .05" then oppc_c_peptideR1=0.05;
    if oppc_c_peptideR="Less than .02" then oppc_c_peptideR1=0.02;
    if oppc_c_peptideR="Less than 0.02" then oppc_c_peptideR1=0.02;
    if (oppc_c_peptideR^="Less than .05" and oppc_c_peptideR^="Less than .02" and oppc_c_peptideR^="Less than 0.02") then oppc_c_peptideR1=oppc_c_peptideR*1;
    
    total_positive_autoab_count1=total_positive_autoab_count;
    if mIAA_Result="Positive" and donortype="T1D" then total_positive_autoab_count1=total_positive_autoab_count-1;
    if mIAA_Result="Positive" and donortype="T1D Medalist" then total_positive_autoab_count1=total_positive_autoab_count-1;
    
    
    /*need to convert hba1c at marthas request and present 2 different ways, based on equation found at http://www.ngsp.org/convert1.asp*/

    oppc_hba1cR1=.;
    oppc_hba1cR1=(oppc_hba1cR-2.152)/(0.09148);
    
    
    
        dr4dq0302=.;
    if drb1_1^="" and drb1_2^="" and dqb1_1^="" and dqb1_2^="" then dr4dq0302=0;
    if 
    (index(DRB1_1, "04:")> 0 OR index(DRB1_1, "040")> 0 OR index(DRB1_1, "041")> 0 OR 
    index(DRB1_2, "04:")> 0 OR index(DRB1_2, "040")> 0 OR index(DRB1_2, "041")> 0) 
    AND
    (INDEX(DQB1_1, "0302")>0 OR INDEX(DQB1_1, "03:02") > 0 OR INDEX(DQB1_1, "03:02/3") > 0 OR 
     INDEX(DQB1_2, "0302")>0 OR INDEX(DQB1_2, "03:02") > 0 OR INDEX(DQB1_2, "03:02/3") > 0)
    then dr4dq0302=1;

    dr0301dq0201=.;
    if drb1_1^="" and drb1_2^="" and dqb1_1^="" and dqb1_2^="" then dr0301dq0201=0;
    if 
    (index(DRB1_1, "03:01")> 0 OR index(DRB1_1, "03:01/5")> 0 OR index(DRB1_1, "0301")> 0 OR  
     index(DRB1_2, "03:01")> 0 OR index(DRB1_2, "03:01/5")> 0 OR index(DRB1_2, "0301")> 0)   
    AND 
    (INDEX(DQB1_1, "02:01")>0 OR INDEX(DQB1_1, "0201") > 0 OR
     INDEX(DQB1_2, "02:01")>0 OR INDEX(DQB1_2, "0201") > 0)
    then dr0301dq0201=1;


    dr4dq0302_only=.;
    if drb1_1^="" and drb1_2^="" and dqb1_1^="" and dqb1_2^="" then dr4dq0302_only=0;
    if dr4dq0302=1 and dr0301dq0201=0 then dr4dq0302_only=1;

    dr0301dq0201_only=.;
    if drb1_1^="" and drb1_2^="" and dqb1_1^="" and dqb1_2^="" then dr0301dq0201_only=0;
    if dr4dq0302=0 and dr0301dq0201=1 then dr0301dq0201_only=1;

    dr4ordr0301=.;
    if drb1_1^="" and drb1_2^="" and dqb1_1^="" and dqb1_2^="" then dr4ordr0301=0;
    dr4ordr0301=dr4dq0302_only+dr0301dq0201_only;

    dr4anddr0301=.;
    if drb1_1^="" and drb1_2^="" and dqb1_1^="" and dqb1_2^="" then dr4anddr0301=0;
    if (dr4dq0302=1) and (dr0301dq0201=1) then dr4anddr0301=1;

    dr1501dq0602=.;
    if drb1_1^="" and drb1_2^="" and dqb1_1^="" and dqb1_2^="" then dr1501dq0602=0;
    if 
    (index(DRB1_1, "15:01")> 0 OR index(DRB1_1, "1501")> 0 OR index(DRB1_1, "15:01/5")> 0 OR 
     index(DRB1_2, "15:01")> 0 OR index(DRB1_2, "1501")> 0 OR index(DRB1_2, "15:01/5")> 0)
    AND
    (INDEX(DQB1_1, "0302")>0 OR INDEX(DQB1_1, "06:02") > 0 OR INDEX(DQB1_1, "0602") > 0 OR INDEX(DQB1_1, "06:02/4") > 0 OR
     INDEX(DQB1_2, "0302")>0 OR INDEX(DQB1_2, "06:02") > 0 OR INDEX(DQB1_2, "0602") > 0 OR INDEX(DQB1_2, "06:02/4") > 0) 
    then dr1501dq0602=1;
    
    /*add relative pancreas weight*/
    if pancreas_received_intact="FALSE" then relative=.;
    if whole_pancreas_g=. then relative=.;
    if weight_g=. then relative=.;
    weight_g=oppc_weightR*1000;
    relative=whole_pancreas_g/weight_g*100;
    

RUN;
Out[95]:

62                                                         The SAS System                         22:22 Wednesday, November 11, 2020

9511 ods listing close;ods html5 (id=saspy_internal) file=_tomods1 options(bitmap_mode='inline') device=svg style=HTMLBlue;
9511 ! ods graphics on / outputfmt=png;
NOTE: Writing HTML5(SASPY_INTERNAL) Body file: _TOMODS1
9512
9513 DATA clinical1;
9514 set clinical;
9515
9516 oppc_ethnicity1=oppc_Ethnicity;
9517 if oppc_Ethnicity="American Indian/Alaska Native" then oppc_ethnicity1="Other";
9518 if oppc_Ethnicity="Asian" then oppc_ethnicity1="Other";
9519 if oppc_Ethnicity="Multiracial" then oppc_ethnicity1="Other";
9520
9521 *donortype1=compress(donortype,'','s');
9522 donortype1=DonorType;
9523 if DonorType1="Cystic fibrosis" then donortype1="Other";
9524 if DonorType1="Gestational diabetes" then donortype1="Other";
9525 if DonorType1="Pending" then donortype1="Other";
9526 if DonorType1="Pregnancy" then donortype1="Other";
9527
9528 cod4group=99;
9529 if cod_final="" then cod4group='.';
9530 IF cod_final="ANOXIA" then cod4group=1; /*anoxia*/
9531 IF cod_final="CEREBROVASCULAR/STROKE" then cod4group=2; /*cerebrovascular/stroke*/
9532 IF cod_final="Other: Cardiovascular" then cod4group=2; /*cerebrovascular/stroke*/
9533 IF cod_final="Cerebral edema" then cod4group=2; /*cerebrovascular/stroke*/
9534 IF cod_final="HEAD TRAUMA" then cod4group=3; /*head trauma*/
9535 if cod_final="Cystic Fibrosis" then cod4group=4; /*other*/
9536 if cod_final="DKA" then cod4group=4; /*other*/
9537 if cod_final="DKA, cerebral edema" then cod4group=4; /*other*/
9538 if cod_final="Cystic Fibrosis" then cod4group=4; /*other*/
9539 if cod_final="Cystic Fibrosis" then cod4group=4; /*other*/
9540 if cod_final="Cystic Fibrosis" then cod4group=4; /*other*/
9541 if cod_final="Infectious Disease - Bacterial Meningitis" then cod4group=4; /*other*/
9542 if cod_final="Meningitis" then cod4group=4; /*other*/
9543 if cod_final="Perinatal Condition/Birth Defect" then cod4group=4; /*other*/
9544 if cod_final="Respiratory Distress/Failure" then cod4group=4; /*other*/
9545 if cod_final="Spinal Cord Injury" then cod4group=4; /*other*/
9546
9547 oppc_c_peptideR1=.;
9548 if oppc_c_peptideR="Less than .05" then oppc_c_peptideR1=0.05;
9549 if oppc_c_peptideR="Less than .02" then oppc_c_peptideR1=0.02;
9550 if oppc_c_peptideR="Less than 0.02" then oppc_c_peptideR1=0.02;
9551 if (oppc_c_peptideR^="Less than .05" and oppc_c_peptideR^="Less than .02" and oppc_c_peptideR^="Less than 0.02") then
9551 ! oppc_c_peptideR1=oppc_c_peptideR*1;
9552
9553 total_positive_autoab_count1=total_positive_autoab_count;
9554 if mIAA_Result="Positive" and donortype="T1D" then total_positive_autoab_count1=total_positive_autoab_count-1;
9555 if mIAA_Result="Positive" and donortype="T1D Medalist" then
9555 ! total_positive_autoab_count1=total_positive_autoab_count-1;
9556
9557
9558 /*need to convert hba1c at marthas request and present 2 different ways, based on equation found at
9558 ! http://www.ngsp.org/convert1.asp*/
9559
9560 oppc_hba1cR1=.;
9561 oppc_hba1cR1=(oppc_hba1cR-2.152)/(0.09148);
9562
9563
9564
9565 dr4dq0302=.;
9566 if drb1_1^="" and drb1_2^="" and dqb1_1^="" and dqb1_2^="" then dr4dq0302=0;
9567 if
9568 (index(DRB1_1, "04:")> 0 OR index(DRB1_1, "040")> 0 OR index(DRB1_1, "041")> 0 OR
9569 index(DRB1_2, "04:")> 0 OR index(DRB1_2, "040")> 0 OR index(DRB1_2, "041")> 0)
9570 AND
9571 (INDEX(DQB1_1, "0302")>0 OR INDEX(DQB1_1, "03:02") > 0 OR INDEX(DQB1_1, "03:02/3") > 0 OR
9572 INDEX(DQB1_2, "0302")>0 OR INDEX(DQB1_2, "03:02") > 0 OR INDEX(DQB1_2, "03:02/3") > 0)
9573 then dr4dq0302=1;
9574
9575 dr0301dq0201=.;
9576 if drb1_1^="" and drb1_2^="" and dqb1_1^="" and dqb1_2^="" then dr0301dq0201=0;
9577 if
9578 (index(DRB1_1, "03:01")> 0 OR index(DRB1_1, "03:01/5")> 0 OR index(DRB1_1, "0301")> 0 OR
9579 index(DRB1_2, "03:01")> 0 OR index(DRB1_2, "03:01/5")> 0 OR index(DRB1_2, "0301")> 0)
9580 AND
9581 (INDEX(DQB1_1, "02:01")>0 OR INDEX(DQB1_1, "0201") > 0 OR
9582 INDEX(DQB1_2, "02:01")>0 OR INDEX(DQB1_2, "0201") > 0)
9583 then dr0301dq0201=1;
9584
9585
9586 dr4dq0302_only=.;
9587 if drb1_1^="" and drb1_2^="" and dqb1_1^="" and dqb1_2^="" then dr4dq0302_only=0;
9588 if dr4dq0302=1 and dr0301dq0201=0 then dr4dq0302_only=1;
9589
9590 dr0301dq0201_only=.;
9591 if drb1_1^="" and drb1_2^="" and dqb1_1^="" and dqb1_2^="" then dr0301dq0201_only=0;
9592 if dr4dq0302=0 and dr0301dq0201=1 then dr0301dq0201_only=1;
9593
9594 dr4ordr0301=.;
9595 if drb1_1^="" and drb1_2^="" and dqb1_1^="" and dqb1_2^="" then dr4ordr0301=0;
9596 dr4ordr0301=dr4dq0302_only+dr0301dq0201_only;
9597
9598 dr4anddr0301=.;
9599 if drb1_1^="" and drb1_2^="" and dqb1_1^="" and dqb1_2^="" then dr4anddr0301=0;
9600 if (dr4dq0302=1) and (dr0301dq0201=1) then dr4anddr0301=1;
9601
9602 dr1501dq0602=.;
9603 if drb1_1^="" and drb1_2^="" and dqb1_1^="" and dqb1_2^="" then dr1501dq0602=0;
9604 if
9605 (index(DRB1_1, "15:01")> 0 OR index(DRB1_1, "1501")> 0 OR index(DRB1_1, "15:01/5")> 0 OR
9606 index(DRB1_2, "15:01")> 0 OR index(DRB1_2, "1501")> 0 OR index(DRB1_2, "15:01/5")> 0)
9607 AND
9608 (INDEX(DQB1_1, "0302")>0 OR INDEX(DQB1_1, "06:02") > 0 OR INDEX(DQB1_1, "0602") > 0 OR INDEX(DQB1_1, "06:02/4") > 0
9608 ! OR
9609 INDEX(DQB1_2, "0302")>0 OR INDEX(DQB1_2, "06:02") > 0 OR INDEX(DQB1_2, "0602") > 0 OR INDEX(DQB1_2, "06:02/4") > 0)
9610 then dr1501dq0602=1;
9611
9612 /*add relative pancreas weight*/
9613 if pancreas_received_intact="FALSE" then relative=.;
9614 if whole_pancreas_g=. then relative=.;
9615 if weight_g=. then relative=.;
9616 weight_g=oppc_weightR*1000;
9617 relative=whole_pancreas_g/weight_g*100;
9618
9619
9620 RUN;

NOTE: Character values have been converted to numeric values at the places given by: (Line):(Column).
9529:36 9551:140
NOTE: Missing values were generated as a result of performing an operation on missing values.
Each place is given by: (Number of times) at (Line):(Column).
52 at 9551:155 299 at 9561:30 100 at 9596:31 67 at 9616:26 152 at 9617:30
NOTE: There were 560 observations read from the data set WORK.CLINICAL.
NOTE: The data set WORK.CLINICAL1 has 560 observations and 76 variables.
NOTE: DATA statement used (Total process time):
real time 0.06 seconds
cpu time 0.07 seconds


9621
9622
9623 ods html5 (id=saspy_internal) close;ods listing;
9624

inspect merged and cleaned file

In [96]:
PROC export data=clinical1 
     outfile="&location\Data\clinical.csv" 
     dbms=csv
     replace;
run;
Out[96]:

63                                                         The SAS System                         22:22 Wednesday, November 11, 2020

9627 ods listing close;ods html5 (id=saspy_internal) file=_tomods1 options(bitmap_mode='inline') device=svg style=HTMLBlue;
9627 ! ods graphics on / outputfmt=png;
NOTE: Writing HTML5(SASPY_INTERNAL) Body file: _TOMODS1
9628
9629 PROC export data=clinical1
9630 outfile="&location\Data\clinical.csv"
9631 dbms=csv
9632 replace;
9633 run;

9634 /**********************************************************************
9635 * PRODUCT: SAS
9636 * VERSION: 9.4
9637 * CREATOR: External File Interface
9638 * DATE: 11NOV20
9639 * DESC: Generated SAS Datastep Code
9640 * TEMPLATE SOURCE: (None Specified.)
9641 ***********************************************************************/
9642 data _null_;
9643 %let _EFIERR_ = 0; /* set the ERROR detection macro variable */
9644 %let _EFIREC_ = 0; /* clear export record count macro variable */
9645 file 'C:\Users\jkaddis\Desktop\pancreas_size\Data\clinical.csv' delimiter=',' DSD DROPOVER lrecl=32767;
9646 if _n_ = 1 then /* write column names or labels */
9647 do;
9648 put
9649 "nPODCaseID"
9650 ','
9651 "DonorType"
9652 ','
9653 "oppc_ageR"
9654 ','
9655 "oppc_Gender"
9656 ','
9657 "oppc_Ethnicity"
9658 ','
9659 "oppc_heightR"
9660 ','
9661 "oppc_weightR"
9662 ','
9663 "oppc_bmiR"
9664 ','
9665 "oppc_abo"
9666 ','
9667 "abo_subtype"
9668 ','
9669 "cod_final"
9670 ','
9671 "DataSets/Demographics/DonorType"
9672 ','
9673 "diabetes_Duration_yrs"
9674 ','
9675 "oppc_C_peptideR"
9676 ','
9677 "oppc_HbA1cR"
9678 ','
9679 "diabetes_history"
9680 ','
9681 "Insulin_depd"
9682 ','
9683 "Insulin_meds_taken"
9684 ','
9685 "Pancreas_Received_Intact"
9686 ','
9687 "whole_pancreas_g"
9688 ','
9689 "panhead_g"
9690 ','
9691 "panbody_g"
9692 ','
9693 "pantail_g"
9694 ','
9695 "Comments"
9696 ','
9697 "hospitalization_stay_minutes"
9698 ','
9699 "hospitalization_stay_days"
9700 ','
9701 "transport_duration_minutes"
9702 ','
9703 "transport_duration_hours"
9704 ','
9705 "date"
9706 ','
9707 "GADA_Result"
9708 ','
9709 "IA_2A_Result"
9710 ','
9711 "mIAA_Result"
9712 ','
9713 "Znt8A_Result"
9714 ','
9715 "Total_Positive_AutoAb_Count"
9716 ','
9717 "Sample"
9718 ','
9719 "Public_Comments"
9720 ','
9721 "Donor Type"
9722 ','
9723 "Transplant(A_1)"
9724 ','
9725 "Transplant(A_2)"
9726 ','
9727 "Transplant(B_1)"
9728 ','
9729 "Transplant(B_2)"
9730 ','
9731 "Transplant(DR_1)"
9732 ','
9733 "Transplant(DR_2)"
9734 ','
9735 "Transplant(DQ_1)"
9736 ','
9737 "Transplant(DQ_2)"
9738 ','
9739 "A_1"
9740 ','
9741 "A_2"
9742 ','
9743 "B_1"
9744 ','
9745 "B_2"
9746 ','
9747 "C_1"
9748 ','
9749 "C_2"
9750 ','
9751 "DRB1_1"
9752 ','
9753 "DRB1_2"
9754 ','
9755 "DQA1_1"
9756 ','
9757 "DQA1_2"
9758 ','
9759 "DQB1_1"
9760 ','
9761 "DQB1_2"
9762 ','
9763 "DPA1_1"
9764 ','
9765 "DPA1_2"
9766 ','
9767 "DPB1_1"
9768 ','
9769 "DPB1_2"
9770 ','
9771 "oppc_ethnicity1"
9772 ','
9773 "donortype1"
9774 ','
9775 "cod4group"
9776 ','
9777 "oppc_c_peptideR1"
9778 ','
9779 "total_positive_autoab_count1"
9780 ','
9781 "oppc_hba1cR1"
9782 ','
9783 "dr4dq0302"
9784 ','
9785 "dr0301dq0201"
9786 ','
9787 "dr4dq0302_only"
9788 ','
9789 "dr0301dq0201_only"
9790 ','
9791 "dr4ordr0301"
9792 ','
9793 "dr4anddr0301"
9794 ','
9795 "dr1501dq0602"
9796 ','
9797 "relative"
9798 ','
9799 "weight_g"
9800 ;
9801 end;
9802 set CLINICAL1 end=EFIEOD;
9803 format nPODCaseID $8. ;
9804 format DonorType $24. ;
9805 format oppc_ageR comma15.4 ;
9806 format oppc_Gender $6. ;
9807 format oppc_Ethnicity $29. ;
9808 format oppc_heightR comma15.4 ;
9809 format oppc_weightR comma15.4 ;
9810 format oppc_bmiR comma15.1 ;
9811 format oppc_abo $3. ;
9812 format abo_subtype $3. ;
9813 format cod_final $50. ;
9814 format "DataSets/Demographics/DonorType"N $24. ;
9815 format diabetes_Duration_yrs best12. ;
9816 format oppc_C_peptideR $14. ;
9817 format oppc_HbA1cR best12. ;
9818 format diabetes_history $20. ;
9819 format Insulin_depd $20. ;
9820 format Insulin_meds_taken $169. ;
9821 format Pancreas_Received_Intact $5. ;
9822 format whole_pancreas_g best12. ;
9823 format panhead_g best12. ;
9824 format panbody_g best12. ;
9825 format pantail_g best12. ;
9826 format Comments $134. ;
9827 format hospitalization_stay_minutes best12. ;
9828 format hospitalization_stay_days comma15.4 ;
9829 format transport_duration_minutes best12. ;
9830 format transport_duration_hours comma15.4 ;
9831 format date date9. ;
9832 format GADA_Result $10. ;
9833 format IA_2A_Result $10. ;
9834 format mIAA_Result $10. ;
9835 format Znt8A_Result $10. ;
9836 format Total_Positive_AutoAb_Count best12. ;
9837 format Sample $16. ;
9838 format Public_Comments $641. ;
9839 format "Donor Type"N $24. ;
9840 format "Transplant(A_1)"N $6. ;
9841 format "Transplant(A_2)"N $6. ;
9842 format "Transplant(B_1)"N $5. ;
9843 format "Transplant(B_2)"N $6. ;
9844 format "Transplant(DR_1)"N $6. ;
9845 format "Transplant(DR_2)"N $6. ;
9846 format "Transplant(DQ_1)"N $6. ;
9847 format "Transplant(DQ_2)"N $6. ;
9848 format A_1 $5. ;
9849 format A_2 $5. ;
9850 format B_1 $5. ;
9851 format B_2 $5. ;
9852 format C_1 $5. ;
9853 format C_2 $5. ;
9854 format DRB1_1 $8. ;
9855 format DRB1_2 $7. ;
9856 format DQA1_1 $7. ;
9857 format DQA1_2 $7. ;
9858 format DQB1_1 $7. ;
9859 format DQB1_2 $7. ;
9860 format DPA1_1 $5. ;
9861 format DPA1_2 $5. ;
9862 format DPB1_1 $5. ;
9863 format DPB1_2 $5. ;
9864 format oppc_ethnicity1 $29. ;
9865 format donortype1 $24. ;
9866 format cod4group best12. ;
9867 format oppc_c_peptideR1 best12. ;
9868 format total_positive_autoab_count1 best12. ;
9869 format oppc_hba1cR1 best12. ;
9870 format dr4dq0302 best12. ;
9871 format dr0301dq0201 best12. ;
9872 format dr4dq0302_only best12. ;
9873 format dr0301dq0201_only best12. ;
9874 format dr4ordr0301 best12. ;
9875 format dr4anddr0301 best12. ;
9876 format dr1501dq0602 best12. ;
9877 format relative best12. ;
9878 format weight_g best12. ;
9879 do;
9880 EFIOUT + 1;
9881 put nPODCaseID $ @;
9882 put DonorType $ @;
9883 put oppc_ageR @;
9884 put oppc_Gender $ @;
9885 put oppc_Ethnicity $ @;
9886 put oppc_heightR @;
9887 put oppc_weightR @;
9888 put oppc_bmiR @;
9889 put oppc_abo $ @;
9890 put abo_subtype $ @;
9891 put cod_final $ @;
9892 put "DataSets/Demographics/DonorType"N $ @;
9893 put diabetes_Duration_yrs @;
9894 put oppc_C_peptideR $ @;
9895 put oppc_HbA1cR @;
9896 put diabetes_history $ @;
9897 put Insulin_depd $ @;
9898 put Insulin_meds_taken $ @;
9899 put Pancreas_Received_Intact $ @;
9900 put whole_pancreas_g @;
9901 put panhead_g @;
9902 put panbody_g @;
9903 put pantail_g @;
9904 put Comments $ @;
9905 put hospitalization_stay_minutes @;
9906 put hospitalization_stay_days @;
9907 put transport_duration_minutes @;
9908 put transport_duration_hours @;
9909 put date @;
9910 put GADA_Result $ @;
9911 put IA_2A_Result $ @;
9912 put mIAA_Result $ @;
9913 put Znt8A_Result $ @;
9914 put Total_Positive_AutoAb_Count @;
9915 put Sample $ @;
9916 put Public_Comments $ @;
9917 put "Donor Type"N $ @;
9918 put "Transplant(A_1)"N $ @;
9919 put "Transplant(A_2)"N $ @;
9920 put "Transplant(B_1)"N $ @;
9921 put "Transplant(B_2)"N $ @;
9922 put "Transplant(DR_1)"N $ @;
9923 put "Transplant(DR_2)"N $ @;
9924 put "Transplant(DQ_1)"N $ @;
9925 put "Transplant(DQ_2)"N $ @;
9926 put A_1 $ @;
9927 put A_2 $ @;
9928 put B_1 $ @;
9929 put B_2 $ @;
9930 put C_1 $ @;
9931 put C_2 $ @;
9932 put DRB1_1 $ @;
9933 put DRB1_2 $ @;
9934 put DQA1_1 $ @;
9935 put DQA1_2 $ @;
9936 put DQB1_1 $ @;
9937 put DQB1_2 $ @;
9938 put DPA1_1 $ @;
9939 put DPA1_2 $ @;
9940 put DPB1_1 $ @;
9941 put DPB1_2 $ @;
9942 put oppc_ethnicity1 $ @;
9943 put donortype1 $ @;
9944 put cod4group @;
9945 put oppc_c_peptideR1 @;
9946 put total_positive_autoab_count1 @;
9947 put oppc_hba1cR1 @;
9948 put dr4dq0302 @;
9949 put dr0301dq0201 @;
9950 put dr4dq0302_only @;
9951 put dr0301dq0201_only @;
9952 put dr4ordr0301 @;
9953 put dr4anddr0301 @;
9954 put dr1501dq0602 @;
9955 put relative @;
9956 put weight_g ;
9957 ;
9958 end;
9959 if _ERROR_ then call symputx('_EFIERR_',1); /* set ERROR detection macro variable */
9960 if EFIEOD then call symputx('_EFIREC_',EFIOUT);
9961 run;

NOTE: The file 'C:\Users\jkaddis\Desktop\pancreas_size\Data\clinical.csv' is:
Filename=C:\Users\jkaddis\Desktop\pancreas_size\Data\clinical.csv,
RECFM=V,LRECL=32767,File Size (bytes)=0,
Last Modified=12Nov2020:01:20:47,
Create Time=11Nov2020:22:23:24

NOTE: 561 records were written to the file 'C:\Users\jkaddis\Desktop\pancreas_size\Data\clinical.csv'.
The minimum record length was 79.
The maximum record length was 1135.
NOTE: There were 560 observations read from the data set WORK.CLINICAL1.
NOTE: DATA statement used (Total process time):
real time 0.09 seconds
cpu time 0.12 seconds


560 records created in C:\Users\jkaddis\Desktop\pancreas_size\Data\clinical.csv from CLINICAL1.


NOTE: "C:\Users\jkaddis\Desktop\pancreas_size\Data\clinical.csv" file was successfully created.
NOTE: PROCEDURE EXPORT used (Total process time):
real time 0.14 seconds
cpu time 0.15 seconds


9962
9963
9964 ods html5 (id=saspy_internal) close;ods listing;
9965

Import study data file. There are two workbooks, split each into a dataset.

In [97]:
PROC import out = cell datafile= 
            "&location\data\Data for John Kaddis-updated 0618.xls"
     dbms =  xls  replace;
     startrow=2;
     namerow=1;
     getnames=yes;
     mixed=yes;
     guessingrows=1000;
     sheet="Area and Cell Analysis";
RUN;


PROC import out = duct datafile= 
            "&location\data\Data for John Kaddis-updated 0618.xls"
     dbms =  xls  replace;
     startrow=2;
     namerow=1;
     getnames=yes;
     mixed=yes;
     guessingrows=1000;
     sheet="Main Duct Size";
RUN;
Out[97]:

64                                                         The SAS System                         22:22 Wednesday, November 11, 2020

9968 ods listing close;ods html5 (id=saspy_internal) file=_tomods1 options(bitmap_mode='inline') device=svg style=HTMLBlue;
9968 ! ods graphics on / outputfmt=png;
NOTE: Writing HTML5(SASPY_INTERNAL) Body file: _TOMODS1
9969
9970 PROC import out = cell datafile=
9971 "&location\data\Data for John Kaddis-updated 0618.xls"
9972 dbms = xls replace;
9973 startrow=2;
9974 namerow=1;
9975 getnames=yes;
9976 mixed=yes;
9977 guessingrows=1000;
9978 sheet="Area and Cell Analysis";
9979 RUN;

NOTE: The import data set has 115 observations and 28 variables.
NOTE: WORK.CELL data set was successfully created.
NOTE: PROCEDURE IMPORT used (Total process time):
real time 0.02 seconds
cpu time 0.01 seconds


9980
9981
9982 PROC import out = duct datafile=
9983 "&location\data\Data for John Kaddis-updated 0618.xls"
9984 dbms = xls replace;
9985 startrow=2;
9986 namerow=1;
9987 getnames=yes;
9988 mixed=yes;
9989 guessingrows=1000;
9990 sheet="Main Duct Size";
9991 RUN;

NOTE: The import data set has 96 observations and 18 variables.
NOTE: WORK.DUCT data set was successfully created.
NOTE: PROCEDURE IMPORT used (Total process time):
real time 0.01 seconds
cpu time 0.04 seconds


9992
9993
9994 ods html5 (id=saspy_internal) close;ods listing;
9995

obtain caseIDs used in both studies

In [98]:
PROC sort data=cell nodupkey out=cell_ids;
by 'Case no.'n;
run;

DATA cell_ids (keep=nPODCaseID);
    set cell_ids;
    nPODCaseID=put ('Case no.'n, 10. -L); /*left align since num to char conversion right aligns*/
RUN;


PROC sort data=duct nodupkey out=duct_ids;
by 'Case no.'n;
run;

DATA duct_ids (keep=nPODCaseID);
    set duct_ids;
    nPODCaseID=put ('Case no.'n, 10. -L); /*left align since num to char conversion right aligns*/
RUN;
Out[98]:

65                                                         The SAS System                         22:22 Wednesday, November 11, 2020

9998 ods listing close;ods html5 (id=saspy_internal) file=_tomods1 options(bitmap_mode='inline') device=svg style=HTMLBlue;
9998 ! ods graphics on / outputfmt=png;
NOTE: Writing HTML5(SASPY_INTERNAL) Body file: _TOMODS1
9999
10000 PROC sort data=cell nodupkey out=cell_ids;
10001 by 'Case no.'n;
10002 run;

NOTE: There were 115 observations read from the data set WORK.CELL.
NOTE: 76 observations with duplicate key values were deleted.
NOTE: The data set WORK.CELL_IDS has 39 observations and 28 variables.
NOTE: PROCEDURE SORT used (Total process time):
real time 0.01 seconds
cpu time 0.01 seconds


10003
10004 DATA cell_ids (keep=nPODCaseID);
10005 set cell_ids;
10006 nPODCaseID=put ('Case no.'n, 10. -L); /*left align since num to char conversion right aligns*/
10007 RUN;

NOTE: There were 39 observations read from the data set WORK.CELL_IDS.
NOTE: The data set WORK.CELL_IDS has 39 observations and 1 variables.
NOTE: DATA statement used (Total process time):
real time 0.01 seconds
cpu time 0.01 seconds


10008
10009
10010 PROC sort data=duct nodupkey out=duct_ids;
10011 by 'Case no.'n;
10012 run;

NOTE: There were 96 observations read from the data set WORK.DUCT.
NOTE: 64 observations with duplicate key values were deleted.
NOTE: The data set WORK.DUCT_IDS has 32 observations and 18 variables.
NOTE: PROCEDURE SORT used (Total process time):
real time 0.01 seconds
cpu time 0.01 seconds


10013
10014 DATA duct_ids (keep=nPODCaseID);
10015 set duct_ids;
10016 nPODCaseID=put ('Case no.'n, 10. -L); /*left align since num to char conversion right aligns*/
10017 RUN;

NOTE: There were 32 observations read from the data set WORK.DUCT_IDS.
NOTE: The data set WORK.DUCT_IDS has 32 observations and 1 variables.
NOTE: DATA statement used (Total process time):
real time 0.01 seconds
cpu time 0.01 seconds


10018
10019
10020 ods html5 (id=saspy_internal) close;ods listing;
10021

clean both study files prior to use

In [99]:
DATA duct1 (drop= 'Case no.'n a group age HbA1c BMI 'Body weight(kg)'n 'Whole Pancreas (g)'n 'Panhead (g)'n 'Panbody (g)'n 'Pantail (g)'n);
    set duct;
    nPODCaseID=put ('Case no.'n, 10. -L); /*left align since num to char conversion right aligns*/
RUN;

DATA cell1 (drop= 'Case no.'n a group age 'Body weight(kg)'n 'Whole Pancreas (g)'n 'Panhead (g)'n 'Panbody (g)'n 'Pantail (g)'n);
    set cell;
    nPODCaseID=put ('Case no.'n, 10. -L); /*left align since num to char conversion right aligns*/
RUN;
Out[99]:

66                                                         The SAS System                         22:22 Wednesday, November 11, 2020

10024 ods listing close;ods html5 (id=saspy_internal) file=_tomods1 options(bitmap_mode='inline') device=svg style=HTMLBlue;
10024 ! ods graphics on / outputfmt=png;
NOTE: Writing HTML5(SASPY_INTERNAL) Body file: _TOMODS1
10025
10026 DATA duct1 (drop= 'Case no.'n a group age HbA1c BMI 'Body weight(kg)'n 'Whole Pancreas (g)'n 'Panhead (g)'n 'Panbody
10026 ! (g)'n 'Pantail (g)'n);
10027 set duct;
10028 nPODCaseID=put ('Case no.'n, 10. -L); /*left align since num to char conversion right aligns*/
10029 RUN;

NOTE: There were 96 observations read from the data set WORK.DUCT.
NOTE: The data set WORK.DUCT1 has 96 observations and 8 variables.
NOTE: DATA statement used (Total process time):
real time 0.01 seconds
cpu time 0.01 seconds


10030
10031 DATA cell1 (drop= 'Case no.'n a group age 'Body weight(kg)'n 'Whole Pancreas (g)'n 'Panhead (g)'n 'Panbody (g)'n 'Pantail
10031 ! (g)'n);
10032 set cell;
10033 nPODCaseID=put ('Case no.'n, 10. -L); /*left align since num to char conversion right aligns*/
10034 RUN;

NOTE: There were 115 observations read from the data set WORK.CELL.
NOTE: The data set WORK.CELL1 has 115 observations and 20 variables.
NOTE: DATA statement used (Total process time):
real time 0.01 seconds
cpu time 0.01 seconds


10035
10036
10037 ods html5 (id=saspy_internal) close;ods listing;
10038

import matching code

In [100]:
PROC import out = cell_match datafile= 
            "&location\data\match_pairs_cells_study.xlsx"
     dbms = xlsx replace;
     getnames=yes;
RUN;

DATA cell_match (keep=nPODCaseID matching_cell);
    set cell_match;
    nPODCaseID=put ('CaseID'n, 10. -L); /*left align since num to char conversion right aligns*/
RUN;
PROC sort data=cell_match;
    by nPODCaseID;
RUN;


PROC import out = duct_match datafile= 
            "&location\data\match_pairs_duct_study.xlsx"
     dbms = xlsx replace;
     getnames=yes;
RUN;


DATA duct_match (keep=nPODCaseID matching_duct);
    set duct_match;
    nPODCaseID=put ('CaseID'n, 10. -L); /*left align since num to char conversion right aligns*/
RUN;
PROC sort data=duct_match;
    by nPODCaseID;
RUN;
Out[100]:

67                                                         The SAS System                         22:22 Wednesday, November 11, 2020

10041 ods listing close;ods html5 (id=saspy_internal) file=_tomods1 options(bitmap_mode='inline') device=svg style=HTMLBlue;
10041 ! ods graphics on / outputfmt=png;
NOTE: Writing HTML5(SASPY_INTERNAL) Body file: _TOMODS1
10042
10043 PROC import out = cell_match datafile=
10044 "&location\data\match_pairs_cells_study.xlsx"
10045 dbms = xlsx replace;
10046 getnames=yes;
10047 RUN;

NOTE: The import data set has 39 observations and 2 variables.
NOTE: WORK.CELL_MATCH data set was successfully created.
NOTE: PROCEDURE IMPORT used (Total process time):
real time 0.01 seconds
cpu time 0.03 seconds


10048
10049 DATA cell_match (keep=nPODCaseID matching_cell);
10050 set cell_match;
10051 nPODCaseID=put ('CaseID'n, 10. -L); /*left align since num to char conversion right aligns*/
10052 RUN;

NOTE: There were 39 observations read from the data set WORK.CELL_MATCH.
NOTE: The data set WORK.CELL_MATCH has 39 observations and 2 variables.
NOTE: DATA statement used (Total process time):
real time 0.01 seconds
cpu time 0.00 seconds


10053 PROC sort data=cell_match;
10054 by nPODCaseID;
10055 RUN;

NOTE: There were 39 observations read from the data set WORK.CELL_MATCH.
NOTE: The data set WORK.CELL_MATCH has 39 observations and 2 variables.
NOTE: PROCEDURE SORT used (Total process time):
real time 0.00 seconds
cpu time 0.00 seconds


10056
10057
10058 PROC import out = duct_match datafile=
10059 "&location\data\match_pairs_duct_study.xlsx"
10060 dbms = xlsx replace;
10061 getnames=yes;
10062 RUN;

NOTE: The import data set has 32 observations and 2 variables.
NOTE: WORK.DUCT_MATCH data set was successfully created.
NOTE: PROCEDURE IMPORT used (Total process time):
real time 0.01 seconds
cpu time 0.00 seconds


10063
10064
10065 DATA duct_match (keep=nPODCaseID matching_duct);
10066 set duct_match;
10067 nPODCaseID=put ('CaseID'n, 10. -L); /*left align since num to char conversion right aligns*/
10068 RUN;

NOTE: There were 32 observations read from the data set WORK.DUCT_MATCH.
NOTE: The data set WORK.DUCT_MATCH has 32 observations and 2 variables.
NOTE: DATA statement used (Total process time):
real time 0.01 seconds
cpu time 0.01 seconds


10069 PROC sort data=duct_match;
10070 by nPODCaseID;
10071 RUN;

NOTE: There were 32 observations read from the data set WORK.DUCT_MATCH.
NOTE: The data set WORK.DUCT_MATCH has 32 observations and 2 variables.
NOTE: PROCEDURE SORT used (Total process time):
real time 0.00 seconds
cpu time 0.00 seconds


10072
10073
10074 ods html5 (id=saspy_internal) close;ods listing;
10075
In [101]:
PROC format;
     value $order
     'No diabetes' = '1_No diabetes'
     'Autoab Pos' = '2_Autoab Pos'
     'T1D' = '3_T1D'
Out[101]:

68                                                         The SAS System                         22:22 Wednesday, November 11, 2020

10078 ods listing close;ods html5 (id=saspy_internal) file=_tomods1 options(bitmap_mode='inline') device=svg style=HTMLBlue;
10078 ! ods graphics on / outputfmt=png;
NOTE: Writing HTML5(SASPY_INTERNAL) Body file: _TOMODS1
10079
10080 PROC format;
10081 value $order
10082 'No diabetes' = '1_No diabetes'
10083 'Autoab Pos' = '2_Autoab Pos'
10084 'T1D' = '3_T1D'
10085
10086
10087 ;
NOTE: Format $ORDER is already on the library WORK.FORMATS.
NOTE: Format $ORDER has been output.
10087 ! *';*";*/;ods html5 (id=saspy_internal) close;ods listing;
10088

supplemental tables 1-3

basic demographics profile of donors for each study

data prep for cell study

In [102]:
/*step1*/

DATA cell_demo;
    merge cell_ids (in=a) clinical1 cell_match ;
    by nPODCaseID;
    if a;
run;

proc export data=cell_demo
     outfile="&location\Data\cell_demo.csv" 
     dbms=csv
     replace;
run; 


/*step 2*/
DATA cell_demo_limited (keep=nPODCaseID Donortype);
    set cell_demo;
RUN;

data cell2;
    merge cell1 (in=a) cell_demo_limited;
    by nPODCaseID;
    if a;
RUN;

DATA cell3;
    set cell2;
    percent_endocrine_area=(('Islet Area (mm²)'n)/('Total Tissue  Area (mm²)'n))*100;
    percent_acinar_area=(('Acinar Area (mm²)'n)/('Total Tissue  Area (mm²)'n))*100;
    percent_remaining_area=(('Duct and other Area (mm²)'n)/('Total Tissue  Area (mm²)'n))*100;
    endocrine_density=('Total islet cell number'n)/('Islet Area (mm²)'n);
    acinar_density=('Total acinar cell numbers'n)/('Acinar Area (mm²)'n);
    endocrine_cell_size='islets: Avg Cell Area (cell size'n;
    acinar_cell_size='acinar: Avg Cell Area (cell size'n;
    donorgroup=donortype;
    if INS=0 and donortype="T1D" then donorgroup="Ins. neg. T1D";
    if INS=1 and donortype="T1D" then donorgroup="Ins. pos. T1D";
RUN;

/*step 3 - figure prep*/


/*althgouh cell size data is quantatative, given inprecise nature of numbers, bin into groups instead of using actual values*/

PROC rank data=cell3 out=cell3 groups=20;
    var endocrine_cell_size; ranks endocrine_cell_size_scale;
RUN;

PROC rank data=cell3 out=cell3 groups=20;
    var acinar_cell_size; ranks acinar_cell_size_scale;
RUN;

/*ranking function above placed data on scale from 0-4, but desired a scale of 1-5 instead*/
DATA cell3;
    set cell3;
    endocrine_cell_size_scale1=endocrine_cell_size_scale+1;
    acinar_cell_size_scale1=acinar_cell_size_scale+1;
RUN;

/*combine data from head, body, and tail into one representative number*/
PROC sort data=cell3;
    by npodcaseid;
run;

proc sql;
create table cell3_combined as
select *, mean(percent_endocrine_area) as mean_percent_endocrine_area,
mean(percent_acinar_area) as mean_percent_acinar_area,
mean(percent_remaining_area) as mean_percent_remaining_area,
mean(endocrine_density) as mean_endocrine_density,
mean(acinar_density) as mean_acinar_density,
mean(endocrine_cell_size) as mean_endocrine_cell_size,
mean(endocrine_cell_size_scale1) as mean_endocrine_cell_size_scale1,
mean(acinar_cell_size_scale1) as mean_acinar_cell_size_scale1
from cell3
group by npodcaseid;
quit;

/*summarize data by donorgroup*/
PROC sort data=cell3_combined;
    by donorgroup;
RUN;

proc sql;
create table cell3_combined_donorgroup as
select *, mean(mean_percent_endocrine_area) as group_percent_endocrine_area,
mean(mean_percent_acinar_area) as group_percent_acinar_area,
mean(mean_percent_remaining_area) as group_percent_remaining_area,
mean(mean_endocrine_density) as group_endocrine_density,
mean(mean_acinar_density) as group_acinar_density,
mean(mean_endocrine_cell_size) as group_endocrine_cell_size,
mean(mean_endocrine_cell_size_scale1) as group_endocrine_cell_size_scale1,
mean(mean_acinar_cell_size_scale1) as group_acinar_cell_size_scale1

from cell3_combined
group by donorgroup;
quit;

/*inspect data*/
proc export data=cell3_combined_donorgroup
     outfile="&location\Data\cell3.csv" 
     dbms=csv
     replace;
run; 


/*prepare data for lollipop chart*/
PROC sort data=cell3_combined_donorgroup out=lollipop NODUPKEY;
    by donorgroup group_percent_endocrine_area group_percent_acinar_area group_percent_remaining_area group_endocrine_density group_acinar_density;
RUN;

proc export data=lollipop
     outfile="&location\Data\cell3_lollipop.csv" 
     dbms=csv
     replace;
run;
Out[102]:

69                                                         The SAS System                         22:22 Wednesday, November 11, 2020

10091 ods listing close;ods html5 (id=saspy_internal) file=_tomods1 options(bitmap_mode='inline') device=svg style=HTMLBlue;
10091 ! ods graphics on / outputfmt=png;
NOTE: Writing HTML5(SASPY_INTERNAL) Body file: _TOMODS1
10092
10093 /*step1*/
10094

NOTE: PROCEDURE FORMAT used (Total process time):
real time 0.21 seconds
cpu time 0.07 seconds


10095 DATA cell_demo;
10096 merge cell_ids (in=a) clinical1 cell_match ;
10097 by nPODCaseID;
10098 if a;
10099 run;

NOTE: There were 39 observations read from the data set WORK.CELL_IDS.
NOTE: There were 560 observations read from the data set WORK.CLINICAL1.
NOTE: There were 39 observations read from the data set WORK.CELL_MATCH.
NOTE: The data set WORK.CELL_DEMO has 39 observations and 77 variables.
NOTE: DATA statement used (Total process time):
real time 0.01 seconds
cpu time 0.01 seconds


10100
10101 proc export data=cell_demo
10102 outfile="&location\Data\cell_demo.csv"
10103 dbms=csv
10104 replace;
10105 run;

10106 /**********************************************************************
10107 * PRODUCT: SAS
10108 * VERSION: 9.4
10109 * CREATOR: External File Interface
10110 * DATE: 11NOV20
10111 * DESC: Generated SAS Datastep Code
10112 * TEMPLATE SOURCE: (None Specified.)
10113 ***********************************************************************/
10114 data _null_;
10115 %let _EFIERR_ = 0; /* set the ERROR detection macro variable */
10116 %let _EFIREC_ = 0; /* clear export record count macro variable */
10117 file 'C:\Users\jkaddis\Desktop\pancreas_size\Data\cell_demo.csv' delimiter=',' DSD DROPOVER lrecl=32767;
10118 if _n_ = 1 then /* write column names or labels */
10119 do;
10120 put
10121 "nPODCaseID"
10122 ','
10123 "DonorType"
10124 ','
10125 "oppc_ageR"
10126 ','
10127 "oppc_Gender"
10128 ','
10129 "oppc_Ethnicity"
10130 ','
10131 "oppc_heightR"
10132 ','
10133 "oppc_weightR"
10134 ','
10135 "oppc_bmiR"
10136 ','
10137 "oppc_abo"
10138 ','
10139 "abo_subtype"
10140 ','
10141 "cod_final"
10142 ','
10143 "DataSets/Demographics/DonorType"
10144 ','
10145 "diabetes_Duration_yrs"
10146 ','
10147 "oppc_C_peptideR"
10148 ','
10149 "oppc_HbA1cR"
10150 ','
10151 "diabetes_history"
10152 ','
10153 "Insulin_depd"
10154 ','
10155 "Insulin_meds_taken"
10156 ','
10157 "Pancreas_Received_Intact"
10158 ','
10159 "whole_pancreas_g"
10160 ','
10161 "panhead_g"
10162 ','
10163 "panbody_g"
10164 ','
10165 "pantail_g"
10166 ','
10167 "Comments"
10168 ','
10169 "hospitalization_stay_minutes"
10170 ','
10171 "hospitalization_stay_days"
10172 ','
10173 "transport_duration_minutes"
10174 ','
10175 "transport_duration_hours"
10176 ','
10177 "date"
10178 ','
10179 "GADA_Result"
10180 ','
10181 "IA_2A_Result"
10182 ','
10183 "mIAA_Result"
10184 ','
10185 "Znt8A_Result"
10186 ','
10187 "Total_Positive_AutoAb_Count"
10188 ','
10189 "Sample"
10190 ','
10191 "Public_Comments"
10192 ','
10193 "Donor Type"
10194 ','
10195 "Transplant(A_1)"
10196 ','
10197 "Transplant(A_2)"
10198 ','
10199 "Transplant(B_1)"
10200 ','
10201 "Transplant(B_2)"
10202 ','
10203 "Transplant(DR_1)"
10204 ','
10205 "Transplant(DR_2)"
10206 ','
10207 "Transplant(DQ_1)"
10208 ','
10209 "Transplant(DQ_2)"
10210 ','
10211 "A_1"
10212 ','
10213 "A_2"
10214 ','
10215 "B_1"
10216 ','
10217 "B_2"
10218 ','
10219 "C_1"
10220 ','
10221 "C_2"
10222 ','
10223 "DRB1_1"
10224 ','
10225 "DRB1_2"
10226 ','
10227 "DQA1_1"
10228 ','
10229 "DQA1_2"
10230 ','
10231 "DQB1_1"
10232 ','
10233 "DQB1_2"
10234 ','
10235 "DPA1_1"
10236 ','
10237 "DPA1_2"
10238 ','
10239 "DPB1_1"
10240 ','
10241 "DPB1_2"
10242 ','
10243 "oppc_ethnicity1"
10244 ','
10245 "donortype1"
10246 ','
10247 "cod4group"
10248 ','
10249 "oppc_c_peptideR1"
10250 ','
10251 "total_positive_autoab_count1"
10252 ','
10253 "oppc_hba1cR1"
10254 ','
10255 "dr4dq0302"
10256 ','
10257 "dr0301dq0201"
10258 ','
10259 "dr4dq0302_only"
10260 ','
10261 "dr0301dq0201_only"
10262 ','
10263 "dr4ordr0301"
10264 ','
10265 "dr4anddr0301"
10266 ','
10267 "dr1501dq0602"
10268 ','
10269 "relative"
10270 ','
10271 "weight_g"
10272 ','
10273 "matching_cell"
10274 ;
10275 end;
10276 set CELL_DEMO end=EFIEOD;
10277 format nPODCaseID $8. ;
10278 format DonorType $24. ;
10279 format oppc_ageR comma15.4 ;
10280 format oppc_Gender $6. ;
10281 format oppc_Ethnicity $29. ;
10282 format oppc_heightR comma15.4 ;
10283 format oppc_weightR comma15.4 ;
10284 format oppc_bmiR comma15.1 ;
10285 format oppc_abo $3. ;
10286 format abo_subtype $3. ;
10287 format cod_final $50. ;
10288 format "DataSets/Demographics/DonorType"N $24. ;
10289 format diabetes_Duration_yrs best12. ;
10290 format oppc_C_peptideR $14. ;
10291 format oppc_HbA1cR best12. ;
10292 format diabetes_history $20. ;
10293 format Insulin_depd $20. ;
10294 format Insulin_meds_taken $169. ;
10295 format Pancreas_Received_Intact $5. ;
10296 format whole_pancreas_g best12. ;
10297 format panhead_g best12. ;
10298 format panbody_g best12. ;
10299 format pantail_g best12. ;
10300 format Comments $134. ;
10301 format hospitalization_stay_minutes best12. ;
10302 format hospitalization_stay_days comma15.4 ;
10303 format transport_duration_minutes best12. ;
10304 format transport_duration_hours comma15.4 ;
10305 format date date9. ;
10306 format GADA_Result $10. ;
10307 format IA_2A_Result $10. ;
10308 format mIAA_Result $10. ;
10309 format Znt8A_Result $10. ;
10310 format Total_Positive_AutoAb_Count best12. ;
10311 format Sample $16. ;
10312 format Public_Comments $641. ;
10313 format "Donor Type"N $24. ;
10314 format "Transplant(A_1)"N $6. ;
10315 format "Transplant(A_2)"N $6. ;
10316 format "Transplant(B_1)"N $5. ;
10317 format "Transplant(B_2)"N $6. ;
10318 format "Transplant(DR_1)"N $6. ;
10319 format "Transplant(DR_2)"N $6. ;
10320 format "Transplant(DQ_1)"N $6. ;
10321 format "Transplant(DQ_2)"N $6. ;
10322 format A_1 $5. ;
10323 format A_2 $5. ;
10324 format B_1 $5. ;
10325 format B_2 $5. ;
10326 format C_1 $5. ;
10327 format C_2 $5. ;
10328 format DRB1_1 $8. ;
10329 format DRB1_2 $7. ;
10330 format DQA1_1 $7. ;
10331 format DQA1_2 $7. ;
10332 format DQB1_1 $7. ;
10333 format DQB1_2 $7. ;
10334 format DPA1_1 $5. ;
10335 format DPA1_2 $5. ;
10336 format DPB1_1 $5. ;
10337 format DPB1_2 $5. ;
10338 format oppc_ethnicity1 $29. ;
10339 format donortype1 $24. ;
10340 format cod4group best12. ;
10341 format oppc_c_peptideR1 best12. ;
10342 format total_positive_autoab_count1 best12. ;
10343 format oppc_hba1cR1 best12. ;
10344 format dr4dq0302 best12. ;
10345 format dr0301dq0201 best12. ;
10346 format dr4dq0302_only best12. ;
10347 format dr0301dq0201_only best12. ;
10348 format dr4ordr0301 best12. ;
10349 format dr4anddr0301 best12. ;
10350 format dr1501dq0602 best12. ;
10351 format relative best12. ;
10352 format weight_g best12. ;
10353 format matching_cell best12. ;
10354 do;
10355 EFIOUT + 1;
10356 put nPODCaseID $ @;
10357 put DonorType $ @;
10358 put oppc_ageR @;
10359 put oppc_Gender $ @;
10360 put oppc_Ethnicity $ @;
10361 put oppc_heightR @;
10362 put oppc_weightR @;
10363 put oppc_bmiR @;
10364 put oppc_abo $ @;
10365 put abo_subtype $ @;
10366 put cod_final $ @;
10367 put "DataSets/Demographics/DonorType"N $ @;
10368 put diabetes_Duration_yrs @;
10369 put oppc_C_peptideR $ @;
10370 put oppc_HbA1cR @;
10371 put diabetes_history $ @;
10372 put Insulin_depd $ @;
10373 put Insulin_meds_taken $ @;
10374 put Pancreas_Received_Intact $ @;
10375 put whole_pancreas_g @;
10376 put panhead_g @;
10377 put panbody_g @;
10378 put pantail_g @;
10379 put Comments $ @;
10380 put hospitalization_stay_minutes @;
10381 put hospitalization_stay_days @;
10382 put transport_duration_minutes @;
10383 put transport_duration_hours @;
10384 put date @;
10385 put GADA_Result $ @;
10386 put IA_2A_Result $ @;
10387 put mIAA_Result $ @;
10388 put Znt8A_Result $ @;
10389 put Total_Positive_AutoAb_Count @;
10390 put Sample $ @;
10391 put Public_Comments $ @;
10392 put "Donor Type"N $ @;
10393 put "Transplant(A_1)"N $ @;
10394 put "Transplant(A_2)"N $ @;
10395 put "Transplant(B_1)"N $ @;
10396 put "Transplant(B_2)"N $ @;
10397 put "Transplant(DR_1)"N $ @;
10398 put "Transplant(DR_2)"N $ @;
10399 put "Transplant(DQ_1)"N $ @;
10400 put "Transplant(DQ_2)"N $ @;
10401 put A_1 $ @;
10402 put A_2 $ @;
10403 put B_1 $ @;
10404 put B_2 $ @;
10405 put C_1 $ @;
10406 put C_2 $ @;
10407 put DRB1_1 $ @;
10408 put DRB1_2 $ @;
10409 put DQA1_1 $ @;
10410 put DQA1_2 $ @;
10411 put DQB1_1 $ @;
10412 put DQB1_2 $ @;
10413 put DPA1_1 $ @;
10414 put DPA1_2 $ @;
10415 put DPB1_1 $ @;
10416 put DPB1_2 $ @;
10417 put oppc_ethnicity1 $ @;
10418 put donortype1 $ @;
10419 put cod4group @;
10420 put oppc_c_peptideR1 @;
10421 put total_positive_autoab_count1 @;
10422 put oppc_hba1cR1 @;
10423 put dr4dq0302 @;
10424 put dr0301dq0201 @;
10425 put dr4dq0302_only @;
10426 put dr0301dq0201_only @;
10427 put dr4ordr0301 @;
10428 put dr4anddr0301 @;
10429 put dr1501dq0602 @;
10430 put relative @;
10431 put weight_g @;
10432 put matching_cell ;
10433 ;
10434 end;
10435 if _ERROR_ then call symputx('_EFIERR_',1); /* set ERROR detection macro variable */
10436 if EFIEOD then call symputx('_EFIREC_',EFIOUT);
10437 run;

NOTE: The file 'C:\Users\jkaddis\Desktop\pancreas_size\Data\cell_demo.csv' is:
Filename=C:\Users\jkaddis\Desktop\pancreas_size\Data\cell_demo.csv,
RECFM=V,LRECL=32767,File Size (bytes)=0,
Last Modified=12Nov2020:01:20:49,
Create Time=12Nov2020:01:20:49

NOTE: 40 records were written to the file 'C:\Users\jkaddis\Desktop\pancreas_size\Data\cell_demo.csv'.
The minimum record length was 352.
The maximum record length was 1124.
NOTE: There were 39 observations read from the data set WORK.CELL_DEMO.
NOTE: DATA statement used (Total process time):
real time 0.07 seconds
cpu time 0.09 seconds


39 records created in C:\Users\jkaddis\Desktop\pancreas_size\Data\cell_demo.csv from CELL_DEMO.


NOTE: "C:\Users\jkaddis\Desktop\pancreas_size\Data\cell_demo.csv" file was successfully created.
NOTE: PROCEDURE EXPORT used (Total process time):
real time 0.12 seconds
cpu time 0.14 seconds


10438
10439
10440 /*step 2*/
10441 DATA cell_demo_limited (keep=nPODCaseID Donortype);
10442 set cell_demo;
10443 RUN;

NOTE: There were 39 observations read from the data set WORK.CELL_DEMO.
NOTE: The data set WORK.CELL_DEMO_LIMITED has 39 observations and 2 variables.
NOTE: DATA statement used (Total process time):
real time 0.01 seconds
cpu time 0.01 seconds


10444
10445 data cell2;
10446 merge cell1 (in=a) cell_demo_limited;
10447 by nPODCaseID;
10448 if a;
10449 RUN;

NOTE: There were 115 observations read from the data set WORK.CELL1.
NOTE: There were 39 observations read from the data set WORK.CELL_DEMO_LIMITED.
NOTE: The data set WORK.CELL2 has 115 observations and 21 variables.
NOTE: DATA statement used (Total process time):
real time 0.01 seconds
cpu time 0.01 seconds


10450
10451 DATA cell3;
10452 set cell2;
10453 percent_endocrine_area=(('Islet Area (mm²)'n)/('Total Tissue Area (mm²)'n))*100;
10454 percent_acinar_area=(('Acinar Area (mm²)'n)/('Total Tissue Area (mm²)'n))*100;
10455 percent_remaining_area=(('Duct and other Area (mm²)'n)/('Total Tissue Area (mm²)'n))*100;
10456 endocrine_density=('Total islet cell number'n)/('Islet Area (mm²)'n);
10457 acinar_density=('Total acinar cell numbers'n)/('Acinar Area (mm²)'n);
10458 endocrine_cell_size='islets: Avg Cell Area (cell size'n;
10459 acinar_cell_size='acinar: Avg Cell Area (cell size'n;
10460 donorgroup=donortype;
10461 if INS=0 and donortype="T1D" then donorgroup="Ins. neg. T1D";
10462 if INS=1 and donortype="T1D" then donorgroup="Ins. pos. T1D";
10463 RUN;

NOTE: There were 115 observations read from the data set WORK.CELL2.
NOTE: The data set WORK.CELL3 has 115 observations and 29 variables.
NOTE: DATA statement used (Total process time):
real time 0.01 seconds
cpu time 0.03 seconds


10464
10465 /*step 3 - figure prep*/
10466
10467
10468 /*althgouh cell size data is quantatative, given inprecise nature of numbers, bin into groups instead of using actual
10468 ! values*/
10469
10470 PROC rank data=cell3 out=cell3 groups=20;
10471 var endocrine_cell_size; ranks endocrine_cell_size_scale;
10472 RUN;

NOTE: The data set WORK.CELL3 has 115 observations and 30 variables.
NOTE: PROCEDURE RANK used (Total process time):
real time 0.01 seconds
cpu time 0.00 seconds


10473
10474 PROC rank data=cell3 out=cell3 groups=20;
10475 var acinar_cell_size; ranks acinar_cell_size_scale;
10476 RUN;

NOTE: The data set WORK.CELL3 has 115 observations and 31 variables.
NOTE: PROCEDURE RANK used (Total process time):
real time 0.01 seconds
cpu time 0.00 seconds


10477
10478 /*ranking function above placed data on scale from 0-4, but desired a scale of 1-5 instead*/
10479 DATA cell3;
10480 set cell3;
10481 endocrine_cell_size_scale1=endocrine_cell_size_scale+1;
10482 acinar_cell_size_scale1=acinar_cell_size_scale+1;
10483 RUN;

NOTE: There were 115 observations read from the data set WORK.CELL3.
NOTE: The data set WORK.CELL3 has 115 observations and 33 variables.
NOTE: DATA statement used (Total process time):
real time 0.01 seconds
cpu time 0.01 seconds


10484
10485 /*combine data from head, body, and tail into one representative number*/
10486 PROC sort data=cell3;
10487 by npodcaseid;
10488 run;

NOTE: There were 115 observations read from the data set WORK.CELL3.
NOTE: The data set WORK.CELL3 has 115 observations and 33 variables.
NOTE: PROCEDURE SORT used (Total process time):
real time 0.00 seconds
cpu time 0.00 seconds


10489
10490 proc sql;
10491 create table cell3_combined as
10492 select *, mean(percent_endocrine_area) as mean_percent_endocrine_area,
10493 mean(percent_acinar_area) as mean_percent_acinar_area,
10494 mean(percent_remaining_area) as mean_percent_remaining_area,
10495 mean(endocrine_density) as mean_endocrine_density,
10496 mean(acinar_density) as mean_acinar_density,
10497 mean(endocrine_cell_size) as mean_endocrine_cell_size,
10498 mean(endocrine_cell_size_scale1) as mean_endocrine_cell_size_scale1,
10499 mean(acinar_cell_size_scale1) as mean_acinar_cell_size_scale1
10500 from cell3
10501 group by npodcaseid;
NOTE: The query requires remerging summary statistics back with the original data.
NOTE: Table WORK.CELL3_COMBINED created, with 115 rows and 41 columns.

10502 quit;
NOTE: PROCEDURE SQL used (Total process time):
real time 0.01 seconds
cpu time 0.00 seconds


10503
10504 /*summarize data by donorgroup*/
10505 PROC sort data=cell3_combined;
10506 by donorgroup;
10507 RUN;

NOTE: There were 115 observations read from the data set WORK.CELL3_COMBINED.
NOTE: The data set WORK.CELL3_COMBINED has 115 observations and 41 variables.
NOTE: PROCEDURE SORT used (Total process time):
real time 0.00 seconds
cpu time 0.00 seconds


10508
10509 proc sql;
10510 create table cell3_combined_donorgroup as
10511 select *, mean(mean_percent_endocrine_area) as group_percent_endocrine_area,
10512 mean(mean_percent_acinar_area) as group_percent_acinar_area,
10513 mean(mean_percent_remaining_area) as group_percent_remaining_area,
10514 mean(mean_endocrine_density) as group_endocrine_density,
10515 mean(mean_acinar_density) as group_acinar_density,
10516 mean(mean_endocrine_cell_size) as group_endocrine_cell_size,
10517 mean(mean_endocrine_cell_size_scale1) as group_endocrine_cell_size_scale1,
10518 mean(mean_acinar_cell_size_scale1) as group_acinar_cell_size_scale1
10519
10520 from cell3_combined
10521 group by donorgroup;
NOTE: The query requires remerging summary statistics back with the original data.
NOTE: Table WORK.CELL3_COMBINED_DONORGROUP created, with 115 rows and 49 columns.

10522 quit;
NOTE: PROCEDURE SQL used (Total process time):
real time 0.01 seconds
cpu time 0.00 seconds


10523
10524 /*inspect data*/
10525 proc export data=cell3_combined_donorgroup
10526 outfile="&location\Data\cell3.csv"
10527 dbms=csv
10528 replace;
10529 run;

10530 /**********************************************************************
10531 * PRODUCT: SAS
10532 * VERSION: 9.4
10533 * CREATOR: External File Interface
10534 * DATE: 11NOV20
10535 * DESC: Generated SAS Datastep Code
10536 * TEMPLATE SOURCE: (None Specified.)
10537 ***********************************************************************/
10538 data _null_;
10539 %let _EFIERR_ = 0; /* set the ERROR detection macro variable */
10540 %let _EFIREC_ = 0; /* clear export record count macro variable */
10541 file 'C:\Users\jkaddis\Desktop\pancreas_size\Data\cell3.csv' delimiter=',' DSD DROPOVER lrecl=32767;
10542 if _n_ = 1 then /* write column names or labels */
10543 do;
10544 put
10545 "region"
10546 ','
10547 "Region_No"
10548 ','
10549 "INS"
10550 ','
10551 "Total Tissue Area (mm²)"
10552 ','
10553 "Islet Area (mm²)"
10554 ','
10555 "Acinar Area (mm²)"
10556 ','
10557 "Duct and other Area (mm²)"
10558 ','
10559 "Islet Area (%) out of total tiss"
10560 ','
10561 "Acinar Area (%) out of total tis"
10562 ','
10563 "Duct and Other (%) out of total"
10564 ','
10565 "Total cells number (acinar +endo"
10566 ','
10567 "Total islet cell number"
10568 ','
10569 "islet:cell density(islet cells/i"
10570 ','
10571 "islets: Avg Cell Area (cell size"
10572 ','
10573 "Total acinar cell numbers"
10574 ','
10575 "acinar:cell density(acinar cells"
10576 ','
10577 "acinar: Avg Cell Area (cell size"
10578 ','
10579 "acinar: Avg Cytoplasm Area (µm²)"
10580 ','
10581 "acinar: Avg Nucleus Area (µm²)"
10582 ','
10583 "nPODCaseID"
10584 ','
10585 "DonorType"
10586 ','
10587 "percent_endocrine_area"
10588 ','
10589 "percent_acinar_area"
10590 ','
10591 "percent_remaining_area"
10592 ','
10593 "endocrine_density"
10594 ','
10595 "acinar_density"
10596 ','
10597 "endocrine_cell_size"
10598 ','
10599 "acinar_cell_size"
10600 ','
10601 "donorgroup"
10602 ','
10603 "endocrine_cell_size_scale"
10604 ','
10605 "acinar_cell_size_scale"
10606 ','
10607 "endocrine_cell_size_scale1"
10608 ','
10609 "acinar_cell_size_scale1"
10610 ','
10611 "mean_percent_endocrine_area"
10612 ','
10613 "mean_percent_acinar_area"
10614 ','
10615 "mean_percent_remaining_area"
10616 ','
10617 "mean_endocrine_density"
10618 ','
10619 "mean_acinar_density"
10620 ','
10621 "mean_endocrine_cell_size"
10622 ','
10623 "mean_endocrine_cell_size_scale1"
10624 ','
10625 "mean_acinar_cell_size_scale1"
10626 ','
10627 "group_percent_endocrine_area"
10628 ','
10629 "group_percent_acinar_area"
10630 ','
10631 "group_percent_remaining_area"
10632 ','
10633 "group_endocrine_density"
10634 ','
10635 "group_acinar_density"
10636 ','
10637 "group_endocrine_cell_size"
10638 ','
10639 "group_endocrine_cell_size_scale1"
10640 ','
10641 "group_acinar_cell_size_scale1"
10642 ;
10643 end;
10644 set CELL3_COMBINED_DONORGROUP end=EFIEOD;
10645 format region $9. ;
10646 format Region_No best14. ;
10647 format INS best10. ;
10648 format "Total Tissue Area (mm²)"N best20. ;
10649 format "Islet Area (mm²)"N best16. ;
10650 format "Acinar Area (mm²)"N best20. ;
10651 format "Duct and other Area (mm²)"N best17. ;
10652 format 'Islet Area (%) out of total tiss'N best20. ;
10653 format 'Acinar Area (%) out of total tis'N best17. ;
10654 format 'Duct and Other (%) out of total'N best20. ;
10655 format "Total cells number (acinar +endo"N best20. ;
10656 format "Total islet cell number"N best19. ;
10657 format "islet:cell density(islet cells/i"N best20. ;
10658 format "islets: Avg Cell Area (cell size"N best20. ;
10659 format "Total acinar cell numbers"N best20. ;
10660 format "acinar:cell density(acinar cells"N best20. ;
10661 format "acinar: Avg Cell Area (cell size"N best20. ;
10662 format "acinar: Avg Cytoplasm Area (µm²)"N best20. ;
10663 format "acinar: Avg Nucleus Area (µm²)"N best20. ;
10664 format nPODCaseID $8. ;
10665 format DonorType $24. ;
10666 format percent_endocrine_area best12. ;
10667 format percent_acinar_area best12. ;
10668 format percent_remaining_area best12. ;
10669 format endocrine_density best12. ;
10670 format acinar_density best12. ;
10671 format endocrine_cell_size best12. ;
10672 format acinar_cell_size best12. ;
10673 format donorgroup $24. ;
10674 format endocrine_cell_size_scale best12. ;
10675 format acinar_cell_size_scale best12. ;
10676 format endocrine_cell_size_scale1 best12. ;
10677 format acinar_cell_size_scale1 best12. ;
10678 format mean_percent_endocrine_area best12. ;
10679 format mean_percent_acinar_area best12. ;
10680 format mean_percent_remaining_area best12. ;
10681 format mean_endocrine_density best12. ;
10682 format mean_acinar_density best12. ;
10683 format mean_endocrine_cell_size best12. ;
10684 format mean_endocrine_cell_size_scale1 best12. ;
10685 format mean_acinar_cell_size_scale1 best12. ;
10686 format group_percent_endocrine_area best12. ;
10687 format group_percent_acinar_area best12. ;
10688 format group_percent_remaining_area best12. ;
10689 format group_endocrine_density best12. ;
10690 format group_acinar_density best12. ;
10691 format group_endocrine_cell_size best12. ;
10692 format group_endocrine_cell_size_scale1 best12. ;
10693 format group_acinar_cell_size_scale1 best12. ;
10694 do;
10695 EFIOUT + 1;
10696 put region $ @;
10697 put Region_No @;
10698 put INS @;
10699 put "Total Tissue Area (mm²)"N @;
10700 put "Islet Area (mm²)"N @;
10701 put "Acinar Area (mm²)"N @;
10702 put "Duct and other Area (mm²)"N @;
10703 put 'Islet Area (%) out of total tiss'N @;
10704 put 'Acinar Area (%) out of total tis'N @;
10705 put 'Duct and Other (%) out of total'N @;
10706 put "Total cells number (acinar +endo"N @;
10707 put "Total islet cell number"N @;
10708 put "islet:cell density(islet cells/i"N @;
10709 put "islets: Avg Cell Area (cell size"N @;
10710 put "Total acinar cell numbers"N @;
10711 put "acinar:cell density(acinar cells"N @;
10712 put "acinar: Avg Cell Area (cell size"N @;
10713 put "acinar: Avg Cytoplasm Area (µm²)"N @;
10714 put "acinar: Avg Nucleus Area (µm²)"N @;
10715 put nPODCaseID $ @;
10716 put DonorType $ @;
10717 put percent_endocrine_area @;
10718 put percent_acinar_area @;
10719 put percent_remaining_area @;
10720 put endocrine_density @;
10721 put acinar_density @;
10722 put endocrine_cell_size @;
10723 put acinar_cell_size @;
10724 put donorgroup $ @;
10725 put endocrine_cell_size_scale @;
10726 put acinar_cell_size_scale @;
10727 put endocrine_cell_size_scale1 @;
10728 put acinar_cell_size_scale1 @;
10729 put mean_percent_endocrine_area @;
10730 put mean_percent_acinar_area @;
10731 put mean_percent_remaining_area @;
10732 put mean_endocrine_density @;
10733 put mean_acinar_density @;
10734 put mean_endocrine_cell_size @;
10735 put mean_endocrine_cell_size_scale1 @;
10736 put mean_acinar_cell_size_scale1 @;
10737 put group_percent_endocrine_area @;
10738 put group_percent_acinar_area @;
10739 put group_percent_remaining_area @;
10740 put group_endocrine_density @;
10741 put group_acinar_density @;
10742 put group_endocrine_cell_size @;
10743 put group_endocrine_cell_size_scale1 @;
10744 put group_acinar_cell_size_scale1 ;
10745 ;
10746 end;
10747 if _ERROR_ then call symputx('_EFIERR_',1); /* set ERROR detection macro variable */
10748 if EFIEOD then call symputx('_EFIREC_',EFIOUT);
10749 run;

NOTE: The file 'C:\Users\jkaddis\Desktop\pancreas_size\Data\cell3.csv' is:
Filename=C:\Users\jkaddis\Desktop\pancreas_size\Data\cell3.csv,
RECFM=V,LRECL=32767,File Size (bytes)=0,
Last Modified=12Nov2020:01:20:49,
Create Time=12Nov2020:01:20:49

NOTE: 116 records were written to the file 'C:\Users\jkaddis\Desktop\pancreas_size\Data\cell3.csv'.
The minimum record length was 463.
The maximum record length was 1179.
NOTE: There were 115 observations read from the data set WORK.CELL3_COMBINED_DONORGROUP.
NOTE: DATA statement used (Total process time):
real time 0.06 seconds
cpu time 0.06 seconds


115 records created in C:\Users\jkaddis\Desktop\pancreas_size\Data\cell3.csv from CELL3_COMBINED_DONORGROUP.


NOTE: "C:\Users\jkaddis\Desktop\pancreas_size\Data\cell3.csv" file was successfully created.
NOTE: PROCEDURE EXPORT used (Total process time):
real time 0.10 seconds
cpu time 0.10 seconds


10750
10751
10752 /*prepare data for lollipop chart*/
10753 PROC sort data=cell3_combined_donorgroup out=lollipop NODUPKEY;
10754 by donorgroup group_percent_endocrine_area group_percent_acinar_area group_percent_remaining_area
10754 ! group_endocrine_density group_acinar_density;
10755 RUN;

NOTE: There were 115 observations read from the data set WORK.CELL3_COMBINED_DONORGROUP.
NOTE: 111 observations with duplicate key values were deleted.
NOTE: The data set WORK.LOLLIPOP has 4 observations and 49 variables.
NOTE: PROCEDURE SORT used (Total process time):
real time 0.00 seconds
cpu time 0.00 seconds


10756
10757 proc export data=lollipop
10758 outfile="&location\Data\cell3_lollipop.csv"
10759 dbms=csv
10760 replace;
10761 run;

10762 /**********************************************************************
10763 * PRODUCT: SAS
10764 * VERSION: 9.4
10765 * CREATOR: External File Interface
10766 * DATE: 11NOV20
10767 * DESC: Generated SAS Datastep Code
10768 * TEMPLATE SOURCE: (None Specified.)
10769 ***********************************************************************/
10770 data _null_;
10771 %let _EFIERR_ = 0; /* set the ERROR detection macro variable */
10772 %let _EFIREC_ = 0; /* clear export record count macro variable */
10773 file 'C:\Users\jkaddis\Desktop\pancreas_size\Data\cell3_lollipop.csv' delimiter=',' DSD DROPOVER lrecl=32767;
10774 if _n_ = 1 then /* write column names or labels */
10775 do;
10776 put
10777 "region"
10778 ','
10779 "Region_No"
10780 ','
10781 "INS"
10782 ','
10783 "Total Tissue Area (mm²)"
10784 ','
10785 "Islet Area (mm²)"
10786 ','
10787 "Acinar Area (mm²)"
10788 ','
10789 "Duct and other Area (mm²)"
10790 ','
10791 "Islet Area (%) out of total tiss"
10792 ','
10793 "Acinar Area (%) out of total tis"
10794 ','
10795 "Duct and Other (%) out of total"
10796 ','
10797 "Total cells number (acinar +endo"
10798 ','
10799 "Total islet cell number"
10800 ','
10801 "islet:cell density(islet cells/i"
10802 ','
10803 "islets: Avg Cell Area (cell size"
10804 ','
10805 "Total acinar cell numbers"
10806 ','
10807 "acinar:cell density(acinar cells"
10808 ','
10809 "acinar: Avg Cell Area (cell size"
10810 ','
10811 "acinar: Avg Cytoplasm Area (µm²)"
10812 ','
10813 "acinar: Avg Nucleus Area (µm²)"
10814 ','
10815 "nPODCaseID"
10816 ','
10817 "DonorType"
10818 ','
10819 "percent_endocrine_area"
10820 ','
10821 "percent_acinar_area"
10822 ','
10823 "percent_remaining_area"
10824 ','
10825 "endocrine_density"
10826 ','
10827 "acinar_density"
10828 ','
10829 "endocrine_cell_size"
10830 ','
10831 "acinar_cell_size"
10832 ','
10833 "donorgroup"
10834 ','
10835 "endocrine_cell_size_scale"
10836 ','
10837 "acinar_cell_size_scale"
10838 ','
10839 "endocrine_cell_size_scale1"
10840 ','
10841 "acinar_cell_size_scale1"
10842 ','
10843 "mean_percent_endocrine_area"
10844 ','
10845 "mean_percent_acinar_area"
10846 ','
10847 "mean_percent_remaining_area"
10848 ','
10849 "mean_endocrine_density"
10850 ','
10851 "mean_acinar_density"
10852 ','
10853 "mean_endocrine_cell_size"
10854 ','
10855 "mean_endocrine_cell_size_scale1"
10856 ','
10857 "mean_acinar_cell_size_scale1"
10858 ','
10859 "group_percent_endocrine_area"
10860 ','
10861 "group_percent_acinar_area"
10862 ','
10863 "group_percent_remaining_area"
10864 ','
10865 "group_endocrine_density"
10866 ','
10867 "group_acinar_density"
10868 ','
10869 "group_endocrine_cell_size"
10870 ','
10871 "group_endocrine_cell_size_scale1"
10872 ','
10873 "group_acinar_cell_size_scale1"
10874 ;
10875 end;
10876 set LOLLIPOP end=EFIEOD;
10877 format region $9. ;
10878 format Region_No best14. ;
10879 format INS best10. ;
10880 format "Total Tissue Area (mm²)"N best20. ;
10881 format "Islet Area (mm²)"N best16. ;
10882 format "Acinar Area (mm²)"N best20. ;
10883 format "Duct and other Area (mm²)"N best17. ;
10884 format 'Islet Area (%) out of total tiss'N best20. ;
10885 format 'Acinar Area (%) out of total tis'N best17. ;
10886 format 'Duct and Other (%) out of total'N best20. ;
10887 format "Total cells number (acinar +endo"N best20. ;
10888 format "Total islet cell number"N best19. ;
10889 format "islet:cell density(islet cells/i"N best20. ;
10890 format "islets: Avg Cell Area (cell size"N best20. ;
10891 format "Total acinar cell numbers"N best20. ;
10892 format "acinar:cell density(acinar cells"N best20. ;
10893 format "acinar: Avg Cell Area (cell size"N best20. ;
10894 format "acinar: Avg Cytoplasm Area (µm²)"N best20. ;
10895 format "acinar: Avg Nucleus Area (µm²)"N best20. ;
10896 format nPODCaseID $8. ;
10897 format DonorType $24. ;
10898 format percent_endocrine_area best12. ;
10899 format percent_acinar_area best12. ;
10900 format percent_remaining_area best12. ;
10901 format endocrine_density best12. ;
10902 format acinar_density best12. ;
10903 format endocrine_cell_size best12. ;
10904 format acinar_cell_size best12. ;
10905 format donorgroup $24. ;
10906 format endocrine_cell_size_scale best12. ;
10907 format acinar_cell_size_scale best12. ;
10908 format endocrine_cell_size_scale1 best12. ;
10909 format acinar_cell_size_scale1 best12. ;
10910 format mean_percent_endocrine_area best12. ;
10911 format mean_percent_acinar_area best12. ;
10912 format mean_percent_remaining_area best12. ;
10913 format mean_endocrine_density best12. ;
10914 format mean_acinar_density best12. ;
10915 format mean_endocrine_cell_size best12. ;
10916 format mean_endocrine_cell_size_scale1 best12. ;
10917 format mean_acinar_cell_size_scale1 best12. ;
10918 format group_percent_endocrine_area best12. ;
10919 format group_percent_acinar_area best12. ;
10920 format group_percent_remaining_area best12. ;
10921 format group_endocrine_density best12. ;
10922 format group_acinar_density best12. ;
10923 format group_endocrine_cell_size best12. ;
10924 format group_endocrine_cell_size_scale1 best12. ;
10925 format group_acinar_cell_size_scale1 best12. ;
10926 do;
10927 EFIOUT + 1;
10928 put region $ @;
10929 put Region_No @;
10930 put INS @;
10931 put "Total Tissue Area (mm²)"N @;
10932 put "Islet Area (mm²)"N @;
10933 put "Acinar Area (mm²)"N @;
10934 put "Duct and other Area (mm²)"N @;
10935 put 'Islet Area (%) out of total tiss'N @;
10936 put 'Acinar Area (%) out of total tis'N @;
10937 put 'Duct and Other (%) out of total'N @;
10938 put "Total cells number (acinar +endo"N @;
10939 put "Total islet cell number"N @;
10940 put "islet:cell density(islet cells/i"N @;
10941 put "islets: Avg Cell Area (cell size"N @;
10942 put "Total acinar cell numbers"N @;
10943 put "acinar:cell density(acinar cells"N @;
10944 put "acinar: Avg Cell Area (cell size"N @;
10945 put "acinar: Avg Cytoplasm Area (µm²)"N @;
10946 put "acinar: Avg Nucleus Area (µm²)"N @;
10947 put nPODCaseID $ @;
10948 put DonorType $ @;
10949 put percent_endocrine_area @;
10950 put percent_acinar_area @;
10951 put percent_remaining_area @;
10952 put endocrine_density @;
10953 put acinar_density @;
10954 put endocrine_cell_size @;
10955 put acinar_cell_size @;
10956 put donorgroup $ @;
10957 put endocrine_cell_size_scale @;
10958 put acinar_cell_size_scale @;
10959 put endocrine_cell_size_scale1 @;
10960 put acinar_cell_size_scale1 @;
10961 put mean_percent_endocrine_area @;
10962 put mean_percent_acinar_area @;
10963 put mean_percent_remaining_area @;
10964 put mean_endocrine_density @;
10965 put mean_acinar_density @;
10966 put mean_endocrine_cell_size @;
10967 put mean_endocrine_cell_size_scale1 @;
10968 put mean_acinar_cell_size_scale1 @;
10969 put group_percent_endocrine_area @;
10970 put group_percent_acinar_area @;
10971 put group_percent_remaining_area @;
10972 put group_endocrine_density @;
10973 put group_acinar_density @;
10974 put group_endocrine_cell_size @;
10975 put group_endocrine_cell_size_scale1 @;
10976 put group_acinar_cell_size_scale1 ;
10977 ;
10978 end;
10979 if _ERROR_ then call symputx('_EFIERR_',1); /* set ERROR detection macro variable */
10980 if EFIEOD then call symputx('_EFIREC_',EFIOUT);
10981 run;

NOTE: The file 'C:\Users\jkaddis\Desktop\pancreas_size\Data\cell3_lollipop.csv' is:
Filename=C:\Users\jkaddis\Desktop\pancreas_size\Data\cell3_lollipop.csv,
RECFM=V,LRECL=32767,File Size (bytes)=0,
Last Modified=12Nov2020:01:20:49,
Create Time=12Nov2020:01:20:49

NOTE: 5 records were written to the file 'C:\Users\jkaddis\Desktop\pancreas_size\Data\cell3_lollipop.csv'.
The minimum record length was 464.
The maximum record length was 1179.
NOTE: There were 4 observations read from the data set WORK.LOLLIPOP.
NOTE: DATA statement used (Total process time):
real time 0.06 seconds
cpu time 0.07 seconds


4 records created in C:\Users\jkaddis\Desktop\pancreas_size\Data\cell3_lollipop.csv from LOLLIPOP.


NOTE: "C:\Users\jkaddis\Desktop\pancreas_size\Data\cell3_lollipop.csv" file was successfully created.
NOTE: PROCEDURE EXPORT used (Total process time):
real time 0.10 seconds
cpu time 0.11 seconds


10982
10983
10984
10985
10986 ods html5 (id=saspy_internal) close;ods listing;
10987

supplemental table 3: cell study

In [103]:
PROC univariate data=cell_demo;
    var oppc_ageR oppc_bmiR  oppc_c_peptideR1 hospitalization_stay_days transport_duration_hours oppc_hba1cr;
RUN;

/*diabetes_duration_yrs not tested*/

/*continuous parametric: ANOVA for multi-group comparisons*/

%macro anova (X); 
proc anova data = cell_demo;
      class DonorType;
      model &X = DonorType;
   run;
%mend anova;

%anova (oppc_ageR);
%anova (oppc_bmiR);
%anova (hospitalization_stay_days);
%anova (transport_duration_hours);
run;

/*continuous non-parametric: wilcoxan rank sum*/

%macro npar1way (X);
proc npar1way data = cell_demo wilcoxon;
  class DonorType;
  var &X;
%mend npar1way;

%npar1way (oppc_c_peptideR1);
%npar1way (oppc_hba1cr);   
run;



/*p-values were calculated for both 2- and multi-class categorical nominal data.  Fisher's exact test was used when values from 1 or more cells in a contingency table (2 x 2 or R x C) were less than 5.  Pearson's chi square was used where values in all cells exceeded 5. If values from 2 or more cells in any table were equal to 0, p-values were not generated.*/

%macro freq (X);
proc freq data=cell_demo;
tables &X*DonorType/measures chisq;
%mend freq;


%macro freq1 (X);
proc freq data=cell_demo;
tables &X*DonorType/measures fisher;
%mend freq1;

%freq1 (oppc_gender); RUN;
%freq1 (dr4dq0302_only);
%freq1 (dr0301dq0201_only);
%freq1 (dr4anddr0301);
%freq1 (dr1501dq0602);


/*oppc_ethnicity1 and cod4group &  total_positive_autoab_count1 not tested due to small smaple size, i.e. valves from 2 cells equaled 0*/


PROC freq data=cell_demo;
    tables donortype;
RUN;



/*data for tables*/

PROC sort data=cell_demo;
    by donortype;
RUN;

PROC means data=cell_demo n mean std;
    var oppc_ageR oppc_bmiR  transport_duration_hours diabetes_duration_yrs;
    by donortype;
RUN;

PROC means data=cell_demo n median min max;
    var oppc_c_peptideR1 hospitalization_stay_days oppc_hba1cR oppc_hba1cR1 ;
    by donortype;
RUN;

PROC freq data=cell_demo ORDER=FORMATTED;
     format donortype $order.;
    tables oppc_gender*donortype oppc_ethnicity1*donortype cod4group*donortype total_positive_autoab_count1*donortype;
RUN;
Out[103]:
SAS Output

SAS Output

The SAS System

The UNIVARIATE Procedure

Variable: oppc_ageR (oppc_ageR)

The UNIVARIATE Procedure

oppc_ageR

Moments

Moments
N 39 Sum Weights 39
Mean 14.265641 Sum Observations 556.36
Std Deviation 5.91241949 Variance 34.9567042
Skewness 0.10605548 Kurtosis -0.9892747
Uncorrected SS 9265.1868 Corrected SS 1328.35476
Coeff Variation 41.4451722 Std Error Mean 0.94674482

Basic Measures of Location and Variability

Basic Statistical Measures
Location Variability
Mean 14.26564 Std Deviation 5.91242
Median 13.00000 Variance 34.95670
Mode 13.00000 Range 20.50000
    Interquartile Range 9.05000

Tests For Location

Tests for Location: Mu0=0
Test Statistic p Value
Student's t t 15.0681 Pr > |t| <.0001
Sign M 19.5 Pr >= |M| <.0001
Signed Rank S 390 Pr >= |S| <.0001

Quantiles

Quantiles (Definition 5)
Level Quantile
100% Max 24.90
99% 24.90
95% 24.00
90% 23.00
75% Q3 19.30
50% Median 13.00
25% Q1 10.25
10% 5.00
5% 4.70
1% 4.40
0% Min 4.40

Extreme Observations

Extreme Observations
Lowest Highest
Value Obs Value Obs
4.40 6 22.1 36
4.70 29 23.0 16
4.80 25 23.3 21
5.00 24 24.0 14
6.73 34 24.9 26

The SAS System

The UNIVARIATE Procedure

Variable: oppc_bmiR (oppc_bmiR)

oppc_bmiR

Moments

Moments
N 39 Sum Weights 39
Mean 22.0066667 Sum Observations 858.26
Std Deviation 6.58680872 Variance 43.3860491
Skewness 2.38853653 Kurtosis 9.59427243
Uncorrected SS 20536.1116 Corrected SS 1648.66987
Coeff Variation 29.9309696 Std Error Mean 1.05473352

Basic Measures of Location and Variability

Basic Statistical Measures
Location Variability
Mean 22.00667 Std Deviation 6.58681
Median 21.70000 Variance 43.38605
Mode 21.90000 Range 38.50000
    Interquartile Range 7.06000

Tests For Location

Tests for Location: Mu0=0
Test Statistic p Value
Student's t t 20.86467 Pr > |t| <.0001
Sign M 19.5 Pr >= |M| <.0001
Signed Rank S 390 Pr >= |S| <.0001

Quantiles

Quantiles (Definition 5)
Level Quantile
100% Max 51.40
99% 51.40
95% 32.50
90% 28.30
75% Q3 24.46
50% Median 21.70
25% Q1 17.40
10% 15.30
5% 14.60
1% 12.90
0% Min 12.90

Extreme Observations

Extreme Observations
Lowest Highest
Value Obs Value Obs
12.9 15 28.2 8
14.6 28 28.3 23
14.8 6 28.5 26
15.3 24 32.5 32
16.2 30 51.4 35

The SAS System

The UNIVARIATE Procedure

Variable: oppc_c_peptideR1

oppc_c_peptideR1

Moments

Moments
N 38 Sum Weights 38
Mean 3.82394737 Sum Observations 145.31
Std Deviation 4.9898267 Variance 24.8983705
Skewness 1.4914636 Kurtosis 1.37213963
Uncorrected SS 1476.8975 Corrected SS 921.239708
Coeff Variation 130.488896 Std Error Mean 0.80945678

Basic Measures of Location and Variability

Basic Statistical Measures
Location Variability
Mean 3.823947 Std Deviation 4.98983
Median 1.800000 Variance 24.89837
Mode 0.050000 Range 17.46000
    Interquartile Range 5.41000

Tests For Location

Tests for Location: Mu0=0
Test Statistic p Value
Student's t t 4.724091 Pr > |t| <.0001
Sign M 19 Pr >= |M| <.0001
Signed Rank S 370.5 Pr >= |S| <.0001

Quantiles

Quantiles (Definition 5)
Level Quantile
100% Max 17.48
99% 17.48
95% 16.59
90% 12.11
75% Q3 5.47
50% Median 1.80
25% Q1 0.06
10% 0.05
5% 0.02
1% 0.02
0% Min 0.02

Extreme Observations

Extreme Observations
Lowest Highest
Value Obs Value Obs
0.02 39 10.56 21
0.02 25 12.11 37
0.05 11 15.33 32
0.05 7 16.59 16
0.05 5 17.48 8

Missing Values

Missing Values
Missing
Value
Count Percent Of
All Obs Missing Obs
. 1 2.56 100.00

The SAS System

The UNIVARIATE Procedure

Variable: hospitalization_stay_days (hospitalization_stay_days)

hospitalization_stay_days

Moments

Moments
N 39 Sum Weights 39
Mean 4.49410256 Sum Observations 175.27
Std Deviation 2.81562998 Variance 7.9277722
Skewness 1.76443846 Kurtosis 3.24404774
Uncorrected SS 1088.9367 Corrected SS 301.255344
Coeff Variation 62.6516628 Std Error Mean 0.45086163

Basic Measures of Location and Variability

Basic Statistical Measures
Location Variability
Mean 4.494103 Std Deviation 2.81563
Median 3.650000 Variance 7.92777
Mode 1.840000 Range 11.95000
    Interquartile Range 3.18000

Tests For Location

Tests for Location: Mu0=0
Test Statistic p Value
Student's t t 9.967809 Pr > |t| <.0001
Sign M 19.5 Pr >= |M| <.0001
Signed Rank S 390 Pr >= |S| <.0001

Quantiles

Quantiles (Definition 5)
Level Quantile
100% Max 13.61
99% 13.61
95% 12.78
90% 7.76
75% Q3 5.87
50% Median 3.65
25% Q1 2.69
10% 1.84
5% 1.71
1% 1.66
0% Min 1.66

Extreme Observations

Extreme Observations
Lowest Highest
Value Obs Value Obs
1.66 12 7.42 10
1.71 14 7.76 26
1.84 17 10.04 9
1.84 7 12.78 31
1.96 4 13.61 20

The SAS System

The UNIVARIATE Procedure

Variable: transport_duration_hours (transport_duration_hours)

transport_duration_hours

Moments

Moments
N 39 Sum Weights 39
Mean 18.9290256 Sum Observations 738.232
Std Deviation 6.07638378 Variance 36.9224398
Skewness 1.65313828 Kurtosis 3.61351151
Uncorrected SS 15377.0652 Corrected SS 1403.05271
Coeff Variation 32.1008798 Std Error Mean 0.97300012

Basic Measures of Location and Variability

Basic Statistical Measures
Location Variability
Mean 18.92903 Std Deviation 6.07638
Median 18.43300 Variance 36.92244
Mode . Range 28.01600
    Interquartile Range 6.05000

Tests For Location

Tests for Location: Mu0=0
Test Statistic p Value
Student's t t 19.45429 Pr > |t| <.0001
Sign M 19.5 Pr >= |M| <.0001
Signed Rank S 390 Pr >= |S| <.0001

Quantiles

Quantiles (Definition 5)
Level Quantile
100% Max 38.883
99% 38.883
95% 36.583
90% 22.983
75% Q3 20.967
50% Median 18.433
25% Q1 14.917
10% 12.267
5% 11.150
1% 10.867
0% Min 10.867

Extreme Observations

Extreme Observations
Lowest Highest
Value Obs Value Obs
10.867 25 22.567 29
11.150 5 22.983 14
12.133 2 32.050 20
12.267 11 36.583 39
12.467 19 38.883 18

The SAS System

The UNIVARIATE Procedure

Variable: oppc_HbA1cR

oppc_HbA1cR

Moments

Moments
N 27 Sum Weights 27
Mean 7.72592593 Sum Observations 208.6
Std Deviation 3.16393044 Variance 10.0104558
Skewness 0.86854506 Kurtosis -0.9422349
Uncorrected SS 1871.9 Corrected SS 260.271852
Coeff Variation 40.9521198 Std Error Mean 0.6088987

Basic Measures of Location and Variability

Basic Statistical Measures
Location Variability
Mean 7.725926 Std Deviation 3.16393
Median 5.600000 Variance 10.01046
Mode 5.300000 Range 8.50000
    Interquartile Range 4.80000

Note: The mode displayed is the smallest of 3 modes with a count of 3.

Tests For Location

Tests for Location: Mu0=0
Test Statistic p Value
Student's t t 12.68836 Pr > |t| <.0001
Sign M 13.5 Pr >= |M| <.0001
Signed Rank S 189 Pr >= |S| <.0001

Quantiles

Quantiles (Definition 5)
Level Quantile
100% Max 13.5
99% 13.5
95% 13.4
90% 13.3
75% Q3 10.2
50% Median 5.6
25% Q1 5.4
10% 5.2
5% 5.1
1% 5.0
0% Min 5.0

Extreme Observations

Extreme Observations
Lowest Highest
Value Obs Value Obs
5.0 16 12.4 1
5.1 33 13.1 13
5.2 19 13.3 9
5.3 30 13.4 31
5.3 29 13.5 28

Missing Values

Missing Values
Missing
Value
Count Percent Of
All Obs Missing Obs
. 12 30.77 100.00

The SAS System

The ANOVA Procedure

The ANOVA Procedure

Data

Class Levels

Class Level Information
Class Levels Values
DonorType 3 Autoab Pos No diabetes T1D

Number of Observations

Number of Observations Read 39
Number of Observations Used 39

The SAS System

The ANOVA Procedure

Dependent Variable: oppc_ageR oppc_ageR

Analysis of Variance

oppc_ageR

Overall ANOVA

Source DF Sum of Squares Mean Square F Value Pr > F
Model 2 60.618640 30.309320 0.86 0.4314
Error 36 1267.736118 35.214892    
Corrected Total 38 1328.354759      

Fit Statistics

R-Square Coeff Var Root MSE oppc_ageR Mean
0.045634 41.59795 5.934214 14.26564

Anova Model ANOVA

Source DF Anova SS Mean Square F Value Pr > F
DonorType 2 60.61864049 30.30932024 0.86 0.4314

Box Plot

Distribution of oppc_ageR by DonorType

The SAS System

The ANOVA Procedure

The ANOVA Procedure

Data

Class Levels

Class Level Information
Class Levels Values
DonorType 3 Autoab Pos No diabetes T1D

Number of Observations

Number of Observations Read 39
Number of Observations Used 39

The SAS System

The ANOVA Procedure

Dependent Variable: oppc_bmiR oppc_bmiR

Analysis of Variance

oppc_bmiR

Overall ANOVA

Source DF Sum of Squares Mean Square F Value Pr > F
Model 2 84.990623 42.495311 0.98 0.3857
Error 36 1563.679244 43.435535    
Corrected Total 38 1648.669867      

Fit Statistics

R-Square Coeff Var Root MSE oppc_bmiR Mean
0.051551 29.94803 6.590564 22.00667

Anova Model ANOVA

Source DF Anova SS Mean Square F Value Pr > F
DonorType 2 84.99062255 42.49531127 0.98 0.3857

Box Plot

Distribution of oppc_bmiR by DonorType

The SAS System

The ANOVA Procedure

The ANOVA Procedure

Data

Class Levels

Class Level Information
Class Levels Values
DonorType 3 Autoab Pos No diabetes T1D

Number of Observations

Number of Observations Read 39
Number of Observations Used 39

The SAS System

The ANOVA Procedure

Dependent Variable: hospitalization_stay_days hospitalization_stay_days

Analysis of Variance

hospitalization_stay_days

Overall ANOVA

Source DF Sum of Squares Mean Square F Value Pr > F
Model 2 0.1662814 0.0831407 0.01 0.9901
Error 36 301.0890622 8.3635851    
Corrected Total 38 301.2553436      

Fit Statistics

R-Square Coeff Var Root MSE hospitalization_stay_days Mean
0.000552 64.35070 2.891986 4.494103

Anova Model ANOVA

Source DF Anova SS Mean Square F Value Pr > F
DonorType 2 0.16628140 0.08314070 0.01 0.9901

Box Plot

Distribution of hospitalization_stay_days by DonorType

The SAS System

The ANOVA Procedure

The ANOVA Procedure

Data

Class Levels

Class Level Information
Class Levels Values
DonorType 3 Autoab Pos No diabetes T1D

Number of Observations

Number of Observations Read 39
Number of Observations Used 39

The SAS System

The ANOVA Procedure

Dependent Variable: transport_duration_hours transport_duration_hours

Analysis of Variance

transport_duration_hours

Overall ANOVA

Source DF Sum of Squares Mean Square F Value Pr > F
Model 2 65.604592 32.802296 0.88 0.4223
Error 36 1337.448121 37.151337    
Corrected Total 38 1403.052713      

Fit Statistics

R-Square Coeff Var Root MSE transport_duration_hours Mean
0.046758 32.20023 6.095190 18.92903

Anova Model ANOVA

Source DF Anova SS Mean Square F Value Pr > F
DonorType 2 65.60459164 32.80229582 0.88 0.4223

Box Plot

Distribution of transport_duration_hours by DonorType

The SAS System

The NPAR1WAY Procedure

The NPAR1WAY Procedure

Variable oppc_c_peptideR1

Wilcoxon Analysis

Scores

Wilcoxon Scores (Rank Sums) for Variable oppc_c_peptideR1
Classified by Variable DonorType
DonorType N Sum of
Scores
Expected
Under H0
Std Dev
Under H0
Mean
Score
Average scores were used for ties.
T1D 16 136.0 312.0 33.754532 8.500
Autoab Pos 8 234.0 156.0 27.871887 29.250
No diabetes 14 371.0 273.0 32.978462 26.500

Kruskal-Wallis Test

Kruskal-Wallis Test
Chi-Square 27.5000
DF 2
Pr > Chi-Square <.0001

Box Plot

Box Plot of Wilcoxon Scores for oppc_c_peptideR1 Classified by DonorType

The SAS System

The NPAR1WAY Procedure

The NPAR1WAY Procedure

Variable oppc_HbA1cR

Wilcoxon Analysis

Scores

Wilcoxon Scores (Rank Sums) for Variable oppc_HbA1cR
Classified by Variable DonorType
DonorType N Sum of
Scores
Expected
Under H0
Std Dev
Under H0
Mean
Score
Average scores were used for ties.
T1D 10 225.0 140.0 19.876936 22.500000
Autoab Pos 6 65.0 84.0 17.112374 10.833333
No diabetes 11 88.0 154.0 20.224664 8.000000

Kruskal-Wallis Test

Kruskal-Wallis Test
Chi-Square 18.7835
DF 2
Pr > Chi-Square <.0001

Box Plot

Box Plot of Wilcoxon Scores for oppc_HbA1cR Classified by DonorType

The SAS System

The FREQ Procedure

The FREQ Procedure

Table oppc_Gender * DonorType

Cross-Tabular Freq Table

Frequency
Percent
Row Pct
Col Pct
Table of oppc_Gender by DonorType
oppc_Gender(oppc_Gender) DonorType(DonorType)
Autoab Pos No diabetes T1D Total
Female
3
7.69
18.75
37.50
5
12.82
31.25
35.71
8
20.51
50.00
47.06
16
41.03
 
 
Male
5
12.82
21.74
62.50
9
23.08
39.13
64.29
9
23.08
39.13
52.94
23
58.97
 
 
Total
8
20.51
14
35.90
17
43.59
39
100.00

Statistics for Table of oppc_Gender by DonorType

Chi-Square Tests

Statistic DF Value Prob
WARNING: 33% of the cells have expected counts less
than 5. Chi-Square may not be a valid test.
Chi-Square 2 0.4601 0.7945
Likelihood Ratio Chi-Square 2 0.4599 0.7946
Mantel-Haenszel Chi-Square 1 0.3004 0.5836
Phi Coefficient   0.1086  
Contingency Coefficient   0.1080  
Cramer's V   0.1086  

Fisher's Exact Test

Fisher's Exact Test
Table Probability (P) 0.0723
Pr <= P 0.9133

Measures of Association

Statistic Value ASE
Gamma -0.1610 0.2705
Kendall's Tau-b -0.0899 0.1517
Stuart's Tau-c -0.0999 0.1688
Somers' D C|R -0.1033 0.1743
Somers' D R|C -0.0782 0.1322
Pearson Correlation -0.0889 0.1597
Spearman Correlation -0.0947 0.1600
Lambda Asymmetric C|R 0.0000 0.1928
Lambda Asymmetric R|C 0.0000 0.0000
Lambda Symmetric 0.0000 0.1116
Uncertainty Coefficient C|R 0.0056 0.0165
Uncertainty Coefficient R|C 0.0087 0.0256
Uncertainty Coefficient Symmetric 0.0068 0.0200

Sample Size = 39


The SAS System

The FREQ Procedure

The FREQ Procedure

Table dr4dq0302_only * DonorType

Cross-Tabular Freq Table

Frequency
Percent
Row Pct
Col Pct
Table of dr4dq0302_only by DonorType
dr4dq0302_only DonorType(DonorType)
Autoab Pos No diabetes T1D Total
0
7
18.42
25.00
87.50
10
26.32
35.71
71.43
11
28.95
39.29
68.75
28
73.68
 
 
1
1
2.63
10.00
12.50
4
10.53
40.00
28.57
5
13.16
50.00
31.25
10
26.32
 
 
Total
8
21.05
14
36.84
16
42.11
38
100.00
Frequency Missing = 1

Statistics for Table of dr4dq0302_only by DonorType

Chi-Square Tests

Statistic DF Value Prob
WARNING: 50% of the cells have expected counts less
than 5. Chi-Square may not be a valid test.
Chi-Square 2 1.0251 0.5990
Likelihood Ratio Chi-Square 2 1.1468 0.5636
Mantel-Haenszel Chi-Square 1 0.8078 0.3688
Phi Coefficient   0.1642  
Contingency Coefficient   0.1621  
Cramer's V   0.1642  

Fisher's Exact Test

Fisher's Exact Test
Table Probability (P) 0.0740
Pr <= P 0.7194

Measures of Association

Statistic Value ASE
Gamma 0.2697 0.2863
Kendall's Tau-b 0.1332 0.1426
Stuart's Tau-c 0.1330 0.1442
Somers' D C|R 0.1714 0.1835
Somers' D R|C 0.1034 0.1116
Pearson Correlation 0.1478 0.1465
Spearman Correlation 0.1405 0.1506
Lambda Asymmetric C|R 0.0000 0.0000
Lambda Asymmetric R|C 0.0000 0.0000
Lambda Symmetric 0.0000 0.0000
Uncertainty Coefficient C|R 0.0142 0.0246
Uncertainty Coefficient R|C 0.0262 0.0452
Uncertainty Coefficient Symmetric 0.0184 0.0319

Effective Sample Size = 38
Frequency Missing = 1


The SAS System

The FREQ Procedure

The FREQ Procedure

Table dr0301dq0201_only * DonorType

Cross-Tabular Freq Table

Frequency
Percent
Row Pct
Col Pct
Table of dr0301dq0201_only by DonorType
dr0301dq0201_only DonorType(DonorType)
Autoab Pos No diabetes T1D Total
0
5
13.16
19.23
62.50
11
28.95
42.31
78.57
10
26.32
38.46
62.50
26
68.42
 
 
1
3
7.89
25.00
37.50
3
7.89
25.00
21.43
6
15.79
50.00
37.50
12
31.58
 
 
Total
8
21.05
14
36.84
16
42.11
38
100.00
Frequency Missing = 1

Statistics for Table of dr0301dq0201_only by DonorType

Chi-Square Tests

Statistic DF Value Prob
WARNING: 33% of the cells have expected counts less
than 5. Chi-Square may not be a valid test.
Chi-Square 2 1.0570 0.5895
Likelihood Ratio Chi-Square 2 1.0945 0.5785
Mantel-Haenszel Chi-Square 1 0.0453 0.8314
Phi Coefficient   0.1668  
Contingency Coefficient   0.1645  
Cramer's V   0.1668  

Fisher's Exact Test

Fisher's Exact Test
Table Probability (P) 0.0603
Pr <= P 0.6609

Measures of Association

Statistic Value ASE
Gamma 0.0882 0.3014
Kendall's Tau-b 0.0473 0.1613
Stuart's Tau-c 0.0499 0.1699
Somers' D C|R 0.0577 0.1965
Somers' D R|C 0.0388 0.1325
Pearson Correlation 0.0350 0.1697
Spearman Correlation 0.0499 0.1701
Lambda Asymmetric C|R 0.0455 0.2035
Lambda Asymmetric R|C 0.0000 0.0000
Lambda Symmetric 0.0294 0.1328
Uncertainty Coefficient C|R 0.0136 0.0254
Uncertainty Coefficient R|C 0.0231 0.0430
Uncertainty Coefficient Symmetric 0.0171 0.0319

Effective Sample Size = 38
Frequency Missing = 1


The SAS System

The FREQ Procedure

The FREQ Procedure

Table dr4anddr0301 * DonorType

Cross-Tabular Freq Table

Frequency
Percent
Row Pct
Col Pct
Table of dr4anddr0301 by DonorType
dr4anddr0301 DonorType(DonorType)
Autoab Pos No diabetes T1D Total
0
7
18.42
21.21
87.50
14
36.84
42.42
100.00
12
31.58
36.36
75.00
33
86.84
 
 
1
1
2.63
20.00
12.50
0
0.00
0.00
0.00
4
10.53
80.00
25.00
5
13.16
 
 
Total
8
21.05
14
36.84
16
42.11
38
100.00
Frequency Missing = 1

Statistics for Table of dr4anddr0301 by DonorType

Chi-Square Tests

Statistic DF Value Prob
WARNING: 50% of the cells have expected counts less
than 5. Chi-Square may not be a valid test.
Chi-Square 2 4.0879 0.1295
Likelihood Ratio Chi-Square 2 5.5696 0.0617
Mantel-Haenszel Chi-Square 1 1.4481 0.2288
Phi Coefficient   0.3280  
Contingency Coefficient   0.3117  
Cramer's V   0.3280  

Fisher's Exact Test

Fisher's Exact Test
Table Probability (P) 0.0290
Pr <= P 0.1308

Measures of Association

Statistic Value ASE
Gamma 0.5273 0.4092
Kendall's Tau-b 0.2096 0.1633
Stuart's Tau-c 0.1607 0.1339
Somers' D C|R 0.3515 0.2652
Somers' D R|C 0.1250 0.1053
Pearson Correlation 0.1978 0.1727
Spearman Correlation 0.2212 0.1720
Lambda Asymmetric C|R 0.0909 0.2210
Lambda Asymmetric R|C 0.0000 0.0000
Lambda Symmetric 0.0741 0.1818
Uncertainty Coefficient C|R 0.0691 0.0354
Uncertainty Coefficient R|C 0.1882 0.0677
Uncertainty Coefficient Symmetric 0.1011 0.0466

Effective Sample Size = 38
Frequency Missing = 1


The SAS System

The FREQ Procedure

The FREQ Procedure

Table dr1501dq0602 * DonorType

Cross-Tabular Freq Table

Frequency
Percent
Row Pct
Col Pct
Table of dr1501dq0602 by DonorType
dr1501dq0602 DonorType(DonorType)
Autoab Pos No diabetes T1D Total
0
7
18.42
20.59
87.50
12
31.58
35.29
85.71
15
39.47
44.12
93.75
34
89.47
 
 
1
1
2.63
25.00
12.50
2
5.26
50.00
14.29
1
2.63
25.00
6.25
4
10.53
 
 
Total
8
21.05
14
36.84
16
42.11
38
100.00
Frequency Missing = 1

Statistics for Table of dr1501dq0602 by DonorType

Chi-Square Tests

Statistic DF Value Prob
WARNING: 50% of the cells have expected counts less
than 5. Chi-Square may not be a valid test.
Chi-Square 2 0.5538 0.7581
Likelihood Ratio Chi-Square 2 0.5808 0.7480
Mantel-Haenszel Chi-Square 1 0.3285 0.5665
Phi Coefficient   0.1207  
Contingency Coefficient   0.1199  
Cramer's V   0.1207  

Fisher's Exact Test

Fisher's Exact Test
Table Probability (P) 0.1578
Pr <= P 0.8179

Measures of Association

Statistic Value ASE
Gamma -0.2667 0.3780
Kendall's Tau-b -0.0955 0.1426
Stuart's Tau-c -0.0665 0.1020
Somers' D C|R -0.1765 0.2605
Somers' D R|C -0.0517 0.0795
Pearson Correlation -0.0942 0.1523
Spearman Correlation -0.1008 0.1504
Lambda Asymmetric C|R 0.0455 0.0769
Lambda Asymmetric R|C 0.0000 0.0000
Lambda Symmetric 0.0385 0.0645
Uncertainty Coefficient C|R 0.0072 0.0183
Uncertainty Coefficient R|C 0.0227 0.0569
Uncertainty Coefficient Symmetric 0.0109 0.0277

Effective Sample Size = 38
Frequency Missing = 1


The SAS System

The FREQ Procedure

The FREQ Procedure

Table DonorType

One-Way Frequencies

DonorType
DonorType Frequency Percent Cumulative
Frequency
Cumulative
Percent
Autoab Pos 8 20.51 8 20.51
No diabetes 14 35.90 22 56.41
T1D 17 43.59 39 100.00

The SAS System

The MEANS Procedure

The MEANS Procedure

DonorType=Autoab Pos

Summary statistics

Variable Label N Mean Std Dev
oppc_ageR
oppc_bmiR
transport_duration_hours
diabetes_Duration_yrs
oppc_ageR
oppc_bmiR
transport_duration_hours
 
8
8
8
0
15.7975000
24.9125000
18.5437500
.
7.9043148
11.4866926
2.4357926
.

DonorType=No diabetes

Summary statistics

Variable Label N Mean Std Dev
oppc_ageR
oppc_bmiR
transport_duration_hours
diabetes_Duration_yrs
oppc_ageR
oppc_bmiR
transport_duration_hours
 
14
14
14
0
12.6664286
21.2400000
20.6131429
.
5.4757586
4.9616623
7.1827008
.

DonorType=T1D

Summary statistics

Variable Label N Mean Std Dev
oppc_ageR
oppc_bmiR
transport_duration_hours
diabetes_Duration_yrs
oppc_ageR
oppc_bmiR
transport_duration_hours
 
17
17
17
17
14.8617647
21.2705882
17.7234118
4.4764706
5.2476045
4.4723826
6.2511551
3.6137808

The SAS System

The MEANS Procedure

The MEANS Procedure

DonorType=Autoab Pos

Summary statistics

Variable Label N Median Minimum Maximum
oppc_c_peptideR1
hospitalization_stay_days
oppc_HbA1cR
oppc_hba1cR1
 
hospitalization_stay_days
 
 
8
8
6
6
6.2200000
4.2300000
5.5500000
37.1447311
1.8400000
2.0400000
5.0000000
31.1324880
17.4800000
6.9000000
5.8000000
39.8775689

DonorType=No diabetes

Summary statistics

Variable Label N Median Minimum Maximum
oppc_c_peptideR1
hospitalization_stay_days
oppc_HbA1cR
oppc_hba1cR1
 
hospitalization_stay_days
 
 
14
14
11
11
4.2400000
3.4000000
5.4000000
35.5050284
1.1700000
1.6600000
5.1000000
32.2256231
15.3300000
13.6100000
6.3000000
45.3432444

DonorType=T1D

Summary statistics

Variable Label N Median Minimum Maximum
oppc_c_peptideR1
hospitalization_stay_days
oppc_HbA1cR
oppc_hba1cR1
 
hospitalization_stay_days
 
 
16
17
10
10
0.0550000
3.5100000
11.4000000
101.0931351
0.0200000
1.7100000
9.5000000
80.3235680
0.4700000
12.7800000
13.5000000
124.0489725

The SAS System

The FREQ Procedure

The FREQ Procedure

Table oppc_Gender * DonorType

Cross-Tabular Freq Table

Frequency
Percent
Row Pct
Col Pct
Table of oppc_Gender by DonorType
oppc_Gender(oppc_Gender) DonorType(DonorType)
1_No diabetes 2_Autoab Pos 3_T1D Total
Female
5
12.82
31.25
35.71
3
7.69
18.75
37.50
8
20.51
50.00
47.06
16
41.03
 
 
Male
9
23.08
39.13
64.29
5
12.82
21.74
62.50
9
23.08
39.13
52.94
23
58.97
 
 
Total
14
35.90
8
20.51
17
43.59
39
100.00

Table oppc_ethnicity1 * DonorType

Cross-Tabular Freq Table

Frequency
Percent
Row Pct
Col Pct
Table of oppc_ethnicity1 by DonorType
oppc_ethnicity1 DonorType(DonorType)
1_No diabetes 2_Autoab Pos 3_T1D Total
African Am
4
10.26
50.00
28.57
2
5.13
25.00
25.00
2
5.13
25.00
11.76
8
20.51
 
 
Caucasian
10
25.64
33.33
71.43
5
12.82
16.67
62.50
15
38.46
50.00
88.24
30
76.92
 
 
Hispanic/Latino
0
0.00
0.00
0.00
1
2.56
100.00
12.50
0
0.00
0.00
0.00
1
2.56
 
 
Total
14
35.90
8
20.51
17
43.59
39
100.00

Table cod4group * DonorType

Cross-Tabular Freq Table

Frequency
Percent
Row Pct
Col Pct
Table of cod4group by DonorType
cod4group DonorType(DonorType)
1_No diabetes 2_Autoab Pos 3_T1D Total
1
6
15.38
42.86
42.86
3
7.69
21.43
37.50
5
12.82
35.71
29.41
14
35.90
 
 
2
0
0.00
0.00
0.00
0
0.00
0.00
0.00
3
7.69
100.00
17.65
3
7.69
 
 
3
7
17.95
41.18
50.00
5
12.82
29.41
62.50
5
12.82
29.41
29.41
17
43.59
 
 
4
1
2.56
20.00
7.14
0
0.00
0.00
0.00
4
10.26
80.00
23.53
5
12.82
 
 
Total
14
35.90
8
20.51
17
43.59
39
100.00

Table total_positive_autoab_count1 * DonorType

Cross-Tabular Freq Table

Frequency
Percent
Row Pct
Col Pct
Table of total_positive_autoab_count1 by DonorType
total_positive_autoab_count1 DonorType(DonorType)
1_No diabetes 2_Autoab Pos 3_T1D Total
0
14
35.90
60.87
100.00
0
0.00
0.00
0.00
9
23.08
39.13
52.94
23
58.97
 
 
1
0
0.00
0.00
0.00
3
7.69
42.86
37.50
4
10.26
57.14
23.53
7
17.95
 
 
2
0
0.00
0.00
0.00
5
12.82
100.00
62.50
0
0.00
0.00
0.00
5
12.82
 
 
3
0
0.00
0.00
0.00
0
0.00
0.00
0.00
4
10.26
100.00
23.53
4
10.26
 
 
Total
14
35.90
8
20.51
17
43.59
39
100.00

supplemental table 2: duct study

In [104]:
/*for duct study*/

DATA duct_demo;
    merge duct_ids (in=a) clinical1 duct_match;
    by nPODCaseID;
    if a;
run;

PROC univariate data=duct_demo;
    var oppc_ageR oppc_bmiR  oppc_c_peptideR1 hospitalization_stay_days transport_duration_hours oppc_hba1cr;
RUN;

proc export data=duct_demo
     outfile="&location\Data\duct_demo.csv" 
     dbms=csv
     replace;
run; 


/*diabetes_duration_yrs not tested*/

/*continuous parametric: 2 group t-test*/
%macro runttest (X);
PROC ttest data=duct_demo;
    class donortype;
    var &X;
RUN;
%mend runttest;

%runttest (oppc_ageR);
%runttest (oppc_bmiR);
%runttest (hospitalization_stay_days);
%runttest (transport_duration_hours);

/*continuous non-parametric: wilcoxon*/


%macro npar1way (X);
proc npar1way data = duct_demo wilcoxon;
  class DonorType;
  var &X;
%mend npar1way;

%npar1way (oppc_c_peptideR1);RUN;
%npar1way (oppc_hba1cr);RUN;


/*p-values were calculated for both 2- and multi-class categorical nominal data.  Fisher's exact test was used when values from 1 or more cells in a contingency table (2 x 2 or R x C) were less than 5.  Pearson's chi square was used where values in all cells exceeded 5. If values from 2 or more cells in any table were equal to 0, p-values were not generated.*/

%macro freq (X);
proc freq data=duct_demo;
tables &X*DonorType/measures chisq;
%mend freq;


%macro freq1 (X);
proc freq data=duct_demo;
tables &X*DonorType/measures fisher;
%mend freq1;

%freq (oppc_gender);RUN;
%freq1 (oppc_ethnicity1);RUN;
%freq1 (cod4group);RUN;
%freq1 (dr4dq0302_only);RUN;
%freq1 (dr0301dq0201_only);RUN;
%freq1 (dr4anddr0301);RUN;
%freq1 (dr1501dq0602);RUN;

PROC freq data=duct_demo;
    tables donortype;
RUN;


/*data for tables*/

PROC sort data=duct_demo;
    by donortype;
RUN;

PROC means data=duct_demo n mean std;
    var oppc_ageR oppc_bmiR  transport_duration_hours diabetes_duration_yrs;
    by donortype;
RUN;

PROC means data=duct_demo n median min max;
    var oppc_c_peptideR1 hospitalization_stay_days oppc_hba1cR oppc_hba1cR1 ;
    by donortype;
RUN;

PROC freq data=duct_demo ORDER=FORMATTED;
     format donortype $order.;
    tables oppc_gender*donortype oppc_ethnicity1*donortype cod4group*donortype total_positive_autoab_count1*donortype;
RUN;
Out[104]:
SAS Output

SAS Output

The SAS System

The UNIVARIATE Procedure

Variable: oppc_ageR (oppc_ageR)

The UNIVARIATE Procedure

oppc_ageR

Moments

Moments
N 32 Sum Weights 32
Mean 13.2021875 Sum Observations 422.47
Std Deviation 5.4071021 Variance 29.2367531
Skewness 0.46608723 Kurtosis -0.1706263
Uncorrected SS 6483.8675 Corrected SS 906.339347
Coeff Variation 40.9561075 Std Error Mean 0.95584964

Basic Measures of Location and Variability

Basic Statistical Measures
Location Variability
Mean 13.20219 Std Deviation 5.40710
Median 12.04000 Variance 29.23675
Mode 13.00000 Range 20.20000
    Interquartile Range 6.82500

Tests For Location

Tests for Location: Mu0=0
Test Statistic p Value
Student's t t 13.81199 Pr > |t| <.0001
Sign M 16 Pr >= |M| <.0001
Signed Rank S 264 Pr >= |S| <.0001

Quantiles

Quantiles (Definition 5)
Level Quantile
100% Max 24.900
99% 24.900
95% 24.000
90% 20.000
75% Q3 17.175
50% Median 12.040
25% Q1 10.350
10% 5.000
5% 4.800
1% 4.700
0% Min 4.700

Extreme Observations

Extreme Observations
Lowest Highest
Value Obs Value Obs
4.7 24 19.3 5
4.8 20 20.0 9
5.0 19 23.3 17
5.0 6 24.0 11
7.9 16 24.9 21

The SAS System

The UNIVARIATE Procedure

Variable: oppc_bmiR (oppc_bmiR)

oppc_bmiR

Moments

Moments
N 32 Sum Weights 32
Mean 20.7425 Sum Observations 663.76
Std Deviation 4.52640924 Variance 20.4883806
Skewness 0.56390346 Kurtosis 0.0656459
Uncorrected SS 14403.1816 Corrected SS 635.1398
Coeff Variation 21.8219079 Std Error Mean 0.80016367

Basic Measures of Location and Variability

Basic Statistical Measures
Location Variability
Mean 20.74250 Std Deviation 4.52641
Median 20.95000 Variance 20.48838
Mode 21.90000 Range 19.60000
    Interquartile Range 7.05000

Tests For Location

Tests for Location: Mu0=0
Test Statistic p Value
Student's t t 25.92282 Pr > |t| <.0001
Sign M 16 Pr >= |M| <.0001
Signed Rank S 264 Pr >= |S| <.0001

Quantiles

Quantiles (Definition 5)
Level Quantile
100% Max 32.50
99% 32.50
95% 28.50
90% 26.10
75% Q3 24.00
50% Median 20.95
25% Q1 16.95
10% 15.90
5% 14.60
1% 12.90
0% Min 12.90

Extreme Observations

Extreme Observations
Lowest Highest
Value Obs Value Obs
12.9 12 25.0 17
14.6 23 26.1 20
15.3 19 28.3 18
15.9 6 28.5 21
16.2 25 32.5 27

The SAS System

The UNIVARIATE Procedure

Variable: oppc_c_peptideR1

oppc_c_peptideR1

Moments

Moments
N 31 Sum Weights 31
Mean 3.73322581 Sum Observations 115.73
Std Deviation 6.4761611 Variance 41.9406626
Skewness 2.94150893 Kurtosis 10.3416004
Uncorrected SS 1690.2661 Corrected SS 1258.21988
Coeff Variation 173.473597 Std Error Mean 1.16315287

Basic Measures of Location and Variability

Basic Statistical Measures
Location Variability
Mean 3.733226 Std Deviation 6.47616
Median 1.170000 Variance 41.94066
Mode 0.050000 Range 31.09000
    Interquartile Range 4.44000

Tests For Location

Tests for Location: Mu0=0
Test Statistic p Value
Student's t t 3.209575 Pr > |t| 0.0032
Sign M 15.5 Pr >= |M| <.0001
Signed Rank S 248 Pr >= |S| <.0001

Quantiles

Quantiles (Definition 5)
Level Quantile
100% Max 31.11
99% 31.11
95% 15.33
90% 10.56
75% Q3 4.54
50% Median 1.17
25% Q1 0.10
10% 0.05
5% 0.02
1% 0.02
0% Min 0.02

Extreme Observations

Extreme Observations
Lowest Highest
Value Obs Value Obs
0.02 32 8.82 19
0.02 20 10.56 17
0.05 5 12.11 30
0.05 4 15.33 27
0.05 3 31.11 29

Missing Values

Missing Values
Missing
Value
Count Percent Of
All Obs Missing Obs
. 1 3.13 100.00

The SAS System

The UNIVARIATE Procedure

Variable: hospitalization_stay_days (hospitalization_stay_days)

hospitalization_stay_days

Moments

Moments
N 31 Sum Weights 31
Mean 4.59741935 Sum Observations 142.52
Std Deviation 3.04988521 Variance 9.30179978
Skewness 1.67536272 Kurtosis 2.60787048
Uncorrected SS 934.2782 Corrected SS 279.053994
Coeff Variation 66.3390692 Std Error Mean 0.54777555

Basic Measures of Location and Variability

Basic Statistical Measures
Location Variability
Mean 4.597419 Std Deviation 3.04989
Median 3.750000 Variance 9.30180
Mode 1.840000 Range 11.95000
    Interquartile Range 3.20000

Tests For Location

Tests for Location: Mu0=0
Test Statistic p Value
Student's t t 8.392889 Pr > |t| <.0001
Sign M 15.5 Pr >= |M| <.0001
Signed Rank S 248 Pr >= |S| <.0001

Quantiles

Quantiles (Definition 5)
Level Quantile
100% Max 13.61
99% 13.61
95% 12.78
90% 7.76
75% Q3 5.87
50% Median 3.75
25% Q1 2.67
10% 1.84
5% 1.71
1% 1.66
0% Min 1.66

Extreme Observations

Extreme Observations
Lowest Highest
Value Obs Value Obs
1.66 9 7.42 8
1.71 11 7.76 21
1.84 13 10.04 7
1.84 5 12.78 26
1.84 1 13.61 16

Missing Values

Missing Values
Missing
Value
Count Percent Of
All Obs Missing Obs
. 1 3.13 100.00

The SAS System

The UNIVARIATE Procedure

Variable: transport_duration_hours (transport_duration_hours)

transport_duration_hours

Moments

Moments
N 31 Sum Weights 31
Mean 19.2284516 Sum Observations 596.082
Std Deviation 6.56663882 Variance 43.1207455
Skewness 1.60914732 Kurtosis 2.8798044
Uncorrected SS 12755.3563 Corrected SS 1293.62236
Coeff Variation 34.1506376 Std Error Mean 1.17940315

Basic Measures of Location and Variability

Basic Statistical Measures
Location Variability
Mean 19.22845 Std Deviation 6.56664
Median 18.43300 Variance 43.12075
Mode . Range 28.01600
    Interquartile Range 7.30000

Tests For Location

Tests for Location: Mu0=0
Test Statistic p Value
Student's t t 16.30354 Pr > |t| <.0001
Sign M 15.5 Pr >= |M| <.0001
Signed Rank S 248 Pr >= |S| <.0001

Quantiles

Quantiles (Definition 5)
Level Quantile
100% Max 38.883
99% 38.883
95% 36.583
90% 22.983
75% Q3 22.217
50% Median 18.433
25% Q1 14.917
10% 13.483
5% 11.183
1% 10.867
0% Min 10.867

Extreme Observations

Extreme Observations
Lowest Highest
Value Obs Value Obs
10.867 20 22.567 24
11.183 31 22.983 11
12.467 15 32.050 16
13.483 10 36.583 32
13.517 25 38.883 14

Missing Values

Missing Values
Missing
Value
Count Percent Of
All Obs Missing Obs
. 1 3.13 100.00

The SAS System

The UNIVARIATE Procedure

Variable: oppc_HbA1cR

oppc_HbA1cR

Moments

Moments
N 22 Sum Weights 22
Mean 8.00909091 Sum Observations 176.2
Std Deviation 3.31776016 Variance 11.0075325
Skewness 0.70711547 Kurtosis -1.2786224
Uncorrected SS 1642.36 Corrected SS 231.158182
Coeff Variation 41.4249282 Std Error Mean 0.70734884

Basic Measures of Location and Variability

Basic Statistical Measures
Location Variability
Mean 8.009091 Std Deviation 3.31776
Median 5.600000 Variance 11.00753
Mode 5.300000 Range 8.40000
    Interquartile Range 4.80000

Note: The mode displayed is the smallest of 2 modes with a count of 3.

Tests For Location

Tests for Location: Mu0=0
Test Statistic p Value
Student's t t 11.32269 Pr > |t| <.0001
Sign M 11 Pr >= |M| <.0001
Signed Rank S 126.5 Pr >= |S| <.0001

Quantiles

Quantiles (Definition 5)
Level Quantile
100% Max 13.5
99% 13.5
95% 13.4
90% 13.3
75% Q3 10.2
50% Median 5.6
25% Q1 5.4
10% 5.3
5% 5.2
1% 5.1
0% Min 5.1

Extreme Observations

Extreme Observations
Lowest Highest
Value Obs Value Obs
5.1 28 12.4 2
5.2 15 13.1 10
5.3 25 13.3 7
5.3 24 13.4 26
5.3 17 13.5 23

Missing Values

Missing Values
Missing
Value
Count Percent Of
All Obs Missing Obs
. 10 31.25 100.00

The TTEST Procedure

oppc_ageR


The SAS System

The TTEST Procedure

Variable: oppc_ageR (oppc_ageR)

Statistics

DonorType N Mean Std Dev Std Err Minimum Maximum
No diabetes 16 12.7950 5.2453 1.3113 4.7000 23.3000
T1D 16 13.6094 5.7057 1.4264 4.8000 24.9000
Diff (1-2)   -0.8144 5.4804 1.9376    

Confidence Limits

DonorType Method Mean 95% CL Mean Std Dev 95% CL Std Dev
No diabetes   12.7950 10.0000 15.5900 5.2453 3.8748 8.1182
T1D   13.6094 10.5690 16.6497 5.7057 4.2149 8.8307
Diff (1-2) Pooled -0.8144 -4.7715 3.1427 5.4804 4.3794 7.3255
Diff (1-2) Satterthwaite -0.8144 -4.7727 3.1439      

T-Tests

Method Variances DF t Value Pr > |t|
Pooled Equal 30 -0.42 0.6773
Satterthwaite Unequal 29.79 -0.42 0.6773

Equality of Variances

Equality of Variances
Method Num DF Den DF F Value Pr > F
Folded F 15 15 1.18 0.7488

Summary Panel

Summary Panel for oppc_ageR

Q-Q Plots

Q-Q Plots for oppc_ageR

The TTEST Procedure

oppc_bmiR


The SAS System

The TTEST Procedure

Variable: oppc_bmiR (oppc_bmiR)

Statistics

DonorType N Mean Std Dev Std Err Minimum Maximum
No diabetes 16 21.2850 4.7661 1.1915 15.3000 32.5000
T1D 16 20.2000 4.3587 1.0897 12.9000 28.5000
Diff (1-2)   1.0850 4.5670 1.6147    

Confidence Limits

DonorType Method Mean 95% CL Mean Std Dev 95% CL Std Dev
No diabetes   21.2850 18.7453 23.8247 4.7661 3.5208 7.3765
T1D   20.2000 17.8774 22.5226 4.3587 3.2198 6.7460
Diff (1-2) Pooled 1.0850 -2.2126 4.3826 4.5670 3.6495 6.1046
Diff (1-2) Satterthwaite 1.0850 -2.2137 4.3837      

T-Tests

Method Variances DF t Value Pr > |t|
Pooled Equal 30 0.67 0.5068
Satterthwaite Unequal 29.764 0.67 0.5068

Equality of Variances

Equality of Variances
Method Num DF Den DF F Value Pr > F
Folded F 15 15 1.20 0.7338

Summary Panel

Summary Panel for oppc_bmiR

Q-Q Plots

Q-Q Plots for oppc_bmiR

The TTEST Procedure

hospitalization_stay_days


The SAS System

The TTEST Procedure

Variable: hospitalization_stay_days (hospitalization_stay_days)

Statistics

DonorType N Mean Std Dev Std Err Minimum Maximum
No diabetes 16 4.5231 2.9644 0.7411 1.6600 13.6100
T1D 15 4.6767 3.2410 0.8368 1.7100 12.7800
Diff (1-2)   -0.1535 3.1010 1.1145    

Confidence Limits

DonorType Method Mean 95% CL Mean Std Dev 95% CL Std Dev
No diabetes   4.5231 2.9435 6.1027 2.9644 2.1898 4.5879
T1D   4.6767 2.8819 6.4715 3.2410 2.3728 5.1114
Diff (1-2) Pooled -0.1535 -2.4329 2.1259 3.1010 2.4697 4.1687
Diff (1-2) Satterthwaite -0.1535 -2.4421 2.1350      

T-Tests

Method Variances DF t Value Pr > |t|
Pooled Equal 29 -0.14 0.8914
Satterthwaite Unequal 28.316 -0.14 0.8917

Equality of Variances

Equality of Variances
Method Num DF Den DF F Value Pr > F
Folded F 14 15 1.20 0.7339

Summary Panel

Summary Panel for hospitalization_stay_days

Q-Q Plots

Q-Q Plots for hospitalization_stay_days

The TTEST Procedure

transport_duration_hours


The SAS System

The TTEST Procedure

Variable: transport_duration_hours (transport_duration_hours)

Statistics

DonorType N Mean Std Dev Std Err Minimum Maximum
No diabetes 16 19.7240 7.1646 1.7911 11.1830 38.8830
T1D 15 18.6999 6.0683 1.5668 10.8670 36.5830
Diff (1-2)   1.0241 6.6579 2.3928    

Confidence Limits

DonorType Method Mean 95% CL Mean Std Dev 95% CL Std Dev
No diabetes   19.7240 15.9063 23.5417 7.1646 5.2925 11.0885
T1D   18.6999 15.3394 22.0604 6.0683 4.4427 9.5703
Diff (1-2) Pooled 1.0241 -3.8698 5.9180 6.6579 5.3024 8.9503
Diff (1-2) Satterthwaite 1.0241 -3.8450 5.8933      

T-Tests

Method Variances DF t Value Pr > |t|
Pooled Equal 29 0.43 0.6718
Satterthwaite Unequal 28.721 0.43 0.6701

Equality of Variances

Equality of Variances
Method Num DF Den DF F Value Pr > F
Folded F 15 14 1.39 0.5402

Summary Panel

Summary Panel for transport_duration_hours

Q-Q Plots

Q-Q Plots for transport_duration_hours

The SAS System

The NPAR1WAY Procedure

The NPAR1WAY Procedure

Variable oppc_c_peptideR1

Wilcoxon Analysis

Scores

Wilcoxon Scores (Rank Sums) for Variable oppc_c_peptideR1
Classified by Variable DonorType
DonorType N Sum of
Scores
Expected
Under H0
Std Dev
Under H0
Mean
Score
Average scores were used for ties.
T1D 15 120.0 240.0 25.280363 8.00
No diabetes 16 376.0 256.0 25.280363 23.50

Two-Sample Test

Wilcoxon Two-Sample Test
Z includes a continuity correction of 0.5.
Statistic 120.0000
   
Normal Approximation  
Z -4.7270
One-Sided Pr < Z <.0001
Two-Sided Pr > |Z| <.0001
   
t Approximation  
One-Sided Pr < Z <.0001
Two-Sided Pr > |Z| <.0001

Kruskal-Wallis Test

Kruskal-Wallis Test
Chi-Square 22.5318
DF 1
Pr > Chi-Square <.0001

Box Plot

Box Plot of Wilcoxon Scores for oppc_c_peptideR1 Classified by DonorType

The SAS System

The NPAR1WAY Procedure

The NPAR1WAY Procedure

Variable oppc_HbA1cR

Wilcoxon Analysis

Scores

Wilcoxon Scores (Rank Sums) for Variable oppc_HbA1cR
Classified by Variable DonorType
DonorType N Sum of
Scores
Expected
Under H0
Std Dev
Under H0
Mean
Score
Average scores were used for ties.
T1D 9 162.0 103.50 14.932641 18.0
No diabetes 13 91.0 149.50 14.932641 7.0

Two-Sample Test

Wilcoxon Two-Sample Test
Z includes a continuity correction of 0.5.
Statistic 162.0000
   
Normal Approximation  
Z 3.8841
One-Sided Pr > Z <.0001
Two-Sided Pr > |Z| 0.0001
   
t Approximation  
One-Sided Pr > Z 0.0004
Two-Sided Pr > |Z| 0.0009

Kruskal-Wallis Test

Kruskal-Wallis Test
Chi-Square 15.3475
DF 1
Pr > Chi-Square <.0001

Box Plot

Box Plot of Wilcoxon Scores for oppc_HbA1cR Classified by DonorType

The SAS System

The FREQ Procedure

The FREQ Procedure

Table oppc_Gender * DonorType

Cross-Tabular Freq Table

Frequency
Percent
Row Pct
Col Pct
Table of oppc_Gender by DonorType
oppc_Gender(oppc_Gender) DonorType(DonorType)
No diabetes T1D Total
Female
5
15.63
41.67
31.25
7
21.88
58.33
43.75
12
37.50
 
 
Male
11
34.38
55.00
68.75
9
28.13
45.00
56.25
20
62.50
 
 
Total
16
50.00
16
50.00
32
100.00

Statistics for Table of oppc_Gender by DonorType

Chi-Square Tests

Statistic DF Value Prob
Chi-Square 1 0.5333 0.4652
Likelihood Ratio Chi-Square 1 0.5352 0.4644
Continuity Adj. Chi-Square 1 0.1333 0.7150
Mantel-Haenszel Chi-Square 1 0.5167 0.4723
Phi Coefficient   -0.1291  
Contingency Coefficient   0.1280  
Cramer's V   -0.1291  

Fisher's Exact Test

Fisher's Exact Test
Cell (1,1) Frequency (F) 5
Left-sided Pr <= F 0.3580
Right-sided Pr >= F 0.8633
   
Table Probability (P) 0.2213
Two-sided Pr <= P 0.7160

Measures of Association

Statistic Value ASE
Gamma -0.2623 0.3437
Kendall's Tau-b -0.1291 0.1750
Stuart's Tau-c -0.1250 0.1697
Somers' D C|R -0.1333 0.1806
Somers' D R|C -0.1250 0.1697
Pearson Correlation -0.1291 0.1750
Spearman Correlation -0.1291 0.1750
Lambda Asymmetric C|R 0.1250 0.2025
Lambda Asymmetric R|C 0.0000 0.0000
Lambda Symmetric 0.0714 0.1181
Uncertainty Coefficient C|R 0.0121 0.0328
Uncertainty Coefficient R|C 0.0126 0.0344
Uncertainty Coefficient Symmetric 0.0123 0.0336

Relative Risk Estimates

Odds Ratio and Relative Risks
Statistic Value 95% Confidence Limits
Odds Ratio 0.5844 0.1375 2.4834
Relative Risk (Column 1) 0.7576 0.3480 1.6494
Relative Risk (Column 2) 1.2963 0.6562 2.5606

Sample Size = 32


The SAS System

The FREQ Procedure

The FREQ Procedure

Table oppc_ethnicity1 * DonorType

Cross-Tabular Freq Table

Frequency
Percent
Row Pct
Col Pct
Table of oppc_ethnicity1 by DonorType
oppc_ethnicity1 DonorType(DonorType)
No diabetes T1D Total
African Am
5
15.63
62.50
31.25
3
9.38
37.50
18.75
8
25.00
 
 
Caucasian
11
34.38
45.83
68.75
13
40.63
54.17
81.25
24
75.00
 
 
Total
16
50.00
16
50.00
32
100.00

Statistics for Table of oppc_ethnicity1 by DonorType

Chi-Square Tests

Statistic DF Value Prob
WARNING: 50% of the cells have expected counts less
than 5. Chi-Square may not be a valid test.
Chi-Square 1 0.6667 0.4142
Likelihood Ratio Chi-Square 1 0.6722 0.4123
Continuity Adj. Chi-Square 1 0.1667 0.6831
Mantel-Haenszel Chi-Square 1 0.6458 0.4216
Phi Coefficient   0.1443  
Contingency Coefficient   0.1429  
Cramer's V   0.1443  

Fisher's Exact Test

Fisher's Exact Test
Cell (1,1) Frequency (F) 5
Left-sided Pr <= F 0.8900
Right-sided Pr >= F 0.3425
   
Table Probability (P) 0.2326
Two-sided Pr <= P 0.6851

Measures of Association

Statistic Value ASE
Gamma 0.3265 0.3740
Kendall's Tau-b 0.1443 0.1731
Stuart's Tau-c 0.1250 0.1515
Somers' D C|R 0.1667 0.1991
Somers' D R|C 0.1250 0.1515
Pearson Correlation 0.1443 0.1731
Spearman Correlation 0.1443 0.1731
Lambda Asymmetric C|R 0.1250 0.2864
Lambda Asymmetric R|C 0.0000 0.0000
Lambda Symmetric 0.0833 0.1956
Uncertainty Coefficient C|R 0.0152 0.0366
Uncertainty Coefficient R|C 0.0187 0.0450
Uncertainty Coefficient Symmetric 0.0167 0.0404

Relative Risk Estimates

Odds Ratio and Relative Risks
Statistic Value 95% Confidence Limits
Odds Ratio 1.9697 0.3816 10.1662
Relative Risk (Column 1) 1.3636 0.6834 2.7210
Relative Risk (Column 2) 0.6923 0.2631 1.8214

Sample Size = 32


The SAS System

The FREQ Procedure

The FREQ Procedure

Table cod4group * DonorType

Cross-Tabular Freq Table

Frequency
Percent
Row Pct
Col Pct
Table of cod4group by DonorType
cod4group DonorType(DonorType)
No diabetes T1D Total
1
6
18.75
66.67
37.50
3
9.38
33.33
18.75
9
28.13
 
 
2
0
0.00
0.00
0.00
4
12.50
100.00
25.00
4
12.50
 
 
3
8
25.00
66.67
50.00
4
12.50
33.33
25.00
12
37.50
 
 
4
2
6.25
28.57
12.50
5
15.63
71.43
31.25
7
21.88
 
 
Total
16
50.00
16
50.00
32
100.00

Statistics for Table of cod4group by DonorType

Chi-Square Tests

Statistic DF Value Prob
WARNING: 75% of the cells have expected counts less
than 5. Chi-Square may not be a valid test.
Chi-Square 3 7.6190 0.0546
Likelihood Ratio Chi-Square 3 9.2521 0.0261
Mantel-Haenszel Chi-Square 1 0.6059 0.4363
Phi Coefficient   0.4880  
Contingency Coefficient   0.4385  
Cramer's V   0.4880  

Fisher's Exact Test

Fisher's Exact Test
Table Probability (P) 0.0015
Pr <= P 0.0640

Measures of Association

Statistic Value ASE
Gamma 0.2041 0.2521
Kendall's Tau-b 0.1305 0.1629
Stuart's Tau-c 0.1563 0.1952
Somers' D C|R 0.1090 0.1361
Somers' D R|C 0.1563 0.1952
Pearson Correlation 0.1398 0.1717
Spearman Correlation 0.1416 0.1768
Lambda Asymmetric C|R 0.4375 0.1555
Lambda Asymmetric R|C 0.0500 0.1462
Lambda Symmetric 0.2222 0.1338
Uncertainty Coefficient C|R 0.2086 0.0990
Uncertainty Coefficient R|C 0.1098 0.0500
Uncertainty Coefficient Symmetric 0.1438 0.0664

Sample Size = 32


The SAS System

The FREQ Procedure

The FREQ Procedure

Table dr4dq0302_only * DonorType

Cross-Tabular Freq Table

Frequency
Percent
Row Pct
Col Pct
Table of dr4dq0302_only by DonorType
dr4dq0302_only DonorType(DonorType)
No diabetes T1D Total
0
11
35.48
45.83
68.75
13
41.94
54.17
86.67
24
77.42
 
 
1
5
16.13
71.43
31.25
2
6.45
28.57
13.33
7
22.58
 
 
Total
16
51.61
15
48.39
31
100.00
Frequency Missing = 1

Statistics for Table of dr4dq0302_only by DonorType

Chi-Square Tests

Statistic DF Value Prob
WARNING: 50% of the cells have expected counts less
than 5. Chi-Square may not be a valid test.
Chi-Square 1 1.4216 0.2331
Likelihood Ratio Chi-Square 1 1.4629 0.2265
Continuity Adj. Chi-Square 1 0.5814 0.4457
Mantel-Haenszel Chi-Square 1 1.3757 0.2408
Phi Coefficient   -0.2141  
Contingency Coefficient   0.2094  
Cramer's V   -0.2141  

Fisher's Exact Test

Fisher's Exact Test
Cell (1,1) Frequency (F) 11
Left-sided Pr <= F 0.2244
Right-sided Pr >= F 0.9500
   
Table Probability (P) 0.1744
Two-sided Pr <= P 0.3944

Measures of Association

Statistic Value ASE
Gamma -0.4943 0.3520
Kendall's Tau-b -0.2141 0.1681
Stuart's Tau-c -0.1790 0.1452
Somers' D C|R -0.2560 0.1987
Somers' D R|C -0.1792 0.1454
Pearson Correlation -0.2141 0.1681
Spearman Correlation -0.2141 0.1681
Lambda Asymmetric C|R 0.1333 0.3040
Lambda Asymmetric R|C 0.0000 0.0000
Lambda Symmetric 0.0909 0.2125
Uncertainty Coefficient C|R 0.0341 0.0548
Uncertainty Coefficient R|C 0.0442 0.0704
Uncertainty Coefficient Symmetric 0.0385 0.0616

Relative Risk Estimates

Odds Ratio and Relative Risks
Statistic Value 95% Confidence Limits
Odds Ratio 0.3385 0.0545 2.1012
Relative Risk (Column 1) 0.6417 0.3386 1.2160
Relative Risk (Column 2) 1.8958 0.5554 6.4715

Effective Sample Size = 31
Frequency Missing = 1


The SAS System

The FREQ Procedure

The FREQ Procedure

Table dr0301dq0201_only * DonorType

Cross-Tabular Freq Table

Frequency
Percent
Row Pct
Col Pct
Table of dr0301dq0201_only by DonorType
dr0301dq0201_only DonorType(DonorType)
No diabetes T1D Total
0
13
41.94
59.09
81.25
9
29.03
40.91
60.00
22
70.97
 
 
1
3
9.68
33.33
18.75
6
19.35
66.67
40.00
9
29.03
 
 
Total
16
51.61
15
48.39
31
100.00
Frequency Missing = 1

Statistics for Table of dr0301dq0201_only by DonorType

Chi-Square Tests

Statistic DF Value Prob
WARNING: 50% of the cells have expected counts less
than 5. Chi-Square may not be a valid test.
Chi-Square 1 1.6968 0.1927
Likelihood Ratio Chi-Square 1 1.7185 0.1899
Continuity Adj. Chi-Square 1 0.8221 0.3646
Mantel-Haenszel Chi-Square 1 1.6420 0.2000
Phi Coefficient   0.2340  
Contingency Coefficient   0.2278  
Cramer's V   0.2340  

Fisher's Exact Test

Fisher's Exact Test
Cell (1,1) Frequency (F) 13
Left-sided Pr <= F 0.9563
Right-sided Pr >= F 0.1827
   
Table Probability (P) 0.1390
Two-sided Pr <= P 0.2524

Measures of Association

Statistic Value ASE
Gamma 0.4857 0.3169
Kendall's Tau-b 0.2340 0.1727
Stuart's Tau-c 0.2123 0.1596
Somers' D C|R 0.2576 0.1889
Somers' D R|C 0.2125 0.1598
Pearson Correlation 0.2340 0.1727
Spearman Correlation 0.2340 0.1727
Lambda Asymmetric C|R 0.2000 0.1789
Lambda Asymmetric R|C 0.0000 0.0000
Lambda Symmetric 0.1250 0.1127
Uncertainty Coefficient C|R 0.0400 0.0600
Uncertainty Coefficient R|C 0.0460 0.0685
Uncertainty Coefficient Symmetric 0.0428 0.0639

Relative Risk Estimates

Odds Ratio and Relative Risks
Statistic Value 95% Confidence Limits
Odds Ratio 2.8889 0.5684 14.6820
Relative Risk (Column 1) 1.7727 0.6606 4.7574
Relative Risk (Column 2) 0.6136 0.3101 1.2141

Effective Sample Size = 31
Frequency Missing = 1


The SAS System

The FREQ Procedure

The FREQ Procedure

Table dr4anddr0301 * DonorType

Cross-Tabular Freq Table

Frequency
Percent
Row Pct
Col Pct
Table of dr4anddr0301 by DonorType
dr4anddr0301 DonorType(DonorType)
No diabetes T1D Total
0
16
51.61
61.54
100.00
10
32.26
38.46
66.67
26
83.87
 
 
1
0
0.00
0.00
0.00
5
16.13
100.00
33.33
5
16.13
 
 
Total
16
51.61
15
48.39
31
100.00
Frequency Missing = 1

Statistics for Table of dr4anddr0301 by DonorType

Chi-Square Tests

Statistic DF Value Prob
WARNING: 50% of the cells have expected counts less
than 5. Chi-Square may not be a valid test.
Chi-Square 1 6.3590 0.0117
Likelihood Ratio Chi-Square 1 8.2964 0.0040
Continuity Adj. Chi-Square 1 4.1336 0.0420
Mantel-Haenszel Chi-Square 1 6.1538 0.0131
Phi Coefficient   0.4529  
Contingency Coefficient   0.4126  
Cramer's V   0.4529  

Fisher's Exact Test

Fisher's Exact Test
Cell (1,1) Frequency (F) 16
Left-sided Pr <= F 1.0000
Right-sided Pr >= F 0.0177
   
Table Probability (P) 0.0177
Two-sided Pr <= P 0.0177

Measures of Association

Statistic Value ASE
Gamma 1.0000 0.0000
Kendall's Tau-b 0.4529 0.1034
Stuart's Tau-c 0.3330 0.1217
Somers' D C|R 0.6154 0.0954
Somers' D R|C 0.3333 0.1217
Pearson Correlation 0.4529 0.1034
Spearman Correlation 0.4529 0.1034
Lambda Asymmetric C|R 0.3333 0.1217
Lambda Asymmetric R|C 0.0000 0.0000
Lambda Symmetric 0.2500 0.0685
Uncertainty Coefficient C|R 0.1932 0.0823
Uncertainty Coefficient R|C 0.3029 0.0797
Uncertainty Coefficient Symmetric 0.2359 0.0829

Relative Risk Estimates

Odds Ratio and Relative Risks
Statistic Value 95% Confidence Limits
One or more statistics not computed -- zero cell.
Relative Risk (Column 2) 0.3846 0.2365 0.6254

Effective Sample Size = 31
Frequency Missing = 1


The SAS System

The FREQ Procedure

The FREQ Procedure

Table dr1501dq0602 * DonorType

Cross-Tabular Freq Table

Frequency
Percent
Row Pct
Col Pct
Table of dr1501dq0602 by DonorType
dr1501dq0602 DonorType(DonorType)
No diabetes T1D Total
0
14
45.16
50.00
87.50
14
45.16
50.00
93.33
28
90.32
 
 
1
2
6.45
66.67
12.50
1
3.23
33.33
6.67
3
9.68
 
 
Total
16
51.61
15
48.39
31
100.00
Frequency Missing = 1

Statistics for Table of dr1501dq0602 by DonorType

Chi-Square Tests

Statistic DF Value Prob
WARNING: 50% of the cells have expected counts less
than 5. Chi-Square may not be a valid test.
Chi-Square 1 0.3014 0.5830
Likelihood Ratio Chi-Square 1 0.3075 0.5792
Continuity Adj. Chi-Square 1 0.0000 1.0000
Mantel-Haenszel Chi-Square 1 0.2917 0.5892
Phi Coefficient   -0.0986  
Contingency Coefficient   0.0981  
Cramer's V   -0.0986  

Fisher's Exact Test

Fisher's Exact Test
Cell (1,1) Frequency (F) 14
Left-sided Pr <= F 0.5250
Right-sided Pr >= F 0.8754
   
Table Probability (P) 0.4004
Two-sided Pr <= P 1.0000

Measures of Association

Statistic Value ASE
Gamma -0.3333 0.5697
Kendall's Tau-b -0.0986 0.1721
Stuart's Tau-c -0.0583 0.1047
Somers' D C|R -0.1667 0.2881
Somers' D R|C -0.0583 0.1048
Pearson Correlation -0.0986 0.1721
Spearman Correlation -0.0986 0.1721
Lambda Asymmetric C|R 0.0000 0.0000
Lambda Asymmetric R|C 0.0000 0.0000
Lambda Symmetric 0.0000 0.0000
Uncertainty Coefficient C|R 0.0072 0.0254
Uncertainty Coefficient R|C 0.0156 0.0549
Uncertainty Coefficient Symmetric 0.0098 0.0347

Relative Risk Estimates

Odds Ratio and Relative Risks
Statistic Value 95% Confidence Limits
Odds Ratio 0.5000 0.0405 6.1658
Relative Risk (Column 1) 0.7500 0.3106 1.8113
Relative Risk (Column 2) 1.5000 0.2902 7.7530

Effective Sample Size = 31
Frequency Missing = 1


The SAS System

The FREQ Procedure

The FREQ Procedure

Table DonorType

One-Way Frequencies

DonorType
DonorType Frequency Percent Cumulative
Frequency
Cumulative
Percent
No diabetes 16 50.00 16 50.00
T1D 16 50.00 32 100.00

The SAS System

The MEANS Procedure

The MEANS Procedure

DonorType=No diabetes

Summary statistics

Variable Label N Mean Std Dev
oppc_ageR
oppc_bmiR
transport_duration_hours
diabetes_Duration_yrs
oppc_ageR
oppc_bmiR
transport_duration_hours
 
16
16
16
0
12.7950000
21.2850000
19.7240000
.
5.2453319
4.7661445
7.1645742
.

DonorType=T1D

Summary statistics

Variable Label N Mean Std Dev
oppc_ageR
oppc_bmiR
transport_duration_hours
diabetes_Duration_yrs
oppc_ageR
oppc_bmiR
transport_duration_hours
 
16
16
15
16
13.6093750
20.2000000
18.6998667
3.0218750
5.7057345
4.3587460
6.0682746
2.7756662

The SAS System

The MEANS Procedure

The MEANS Procedure

DonorType=No diabetes

Summary statistics

Variable Label N Median Minimum Maximum
oppc_c_peptideR1
hospitalization_stay_days
oppc_HbA1cR
oppc_hba1cR1
 
hospitalization_stay_days
 
 
16
16
13
13
4.2400000
3.7000000
5.4000000
35.5050284
1.1700000
1.6600000
5.1000000
32.2256231
31.1100000
13.6100000
6.3000000
45.3432444

DonorType=T1D

Summary statistics

Variable Label N Median Minimum Maximum
oppc_c_peptideR1
hospitalization_stay_days
oppc_HbA1cR
oppc_hba1cR1
 
hospitalization_stay_days
 
 
15
15
9
9
0.1000000
3.9200000
12.4000000
112.0244862
0.0200000
1.7100000
9.5000000
80.3235680
0.4700000
12.7800000
13.5000000
124.0489725

The SAS System

The FREQ Procedure

The FREQ Procedure

Table oppc_Gender * DonorType

Cross-Tabular Freq Table

Frequency
Percent
Row Pct
Col Pct
Table of oppc_Gender by DonorType
oppc_Gender(oppc_Gender) DonorType(DonorType)
1_No diabetes 3_T1D Total
Female
5
15.63
41.67
31.25
7
21.88
58.33
43.75
12
37.50
 
 
Male
11
34.38
55.00
68.75
9
28.13
45.00
56.25
20
62.50
 
 
Total
16
50.00
16
50.00
32
100.00

Table oppc_ethnicity1 * DonorType

Cross-Tabular Freq Table

Frequency
Percent
Row Pct
Col Pct
Table of oppc_ethnicity1 by DonorType
oppc_ethnicity1 DonorType(DonorType)
1_No diabetes 3_T1D Total
African Am
5
15.63
62.50
31.25
3
9.38
37.50
18.75
8
25.00
 
 
Caucasian
11
34.38
45.83
68.75
13
40.63
54.17
81.25
24
75.00
 
 
Total
16
50.00
16
50.00
32
100.00

Table cod4group * DonorType

Cross-Tabular Freq Table

Frequency
Percent
Row Pct
Col Pct
Table of cod4group by DonorType
cod4group DonorType(DonorType)
1_No diabetes 3_T1D Total
1
6
18.75
66.67
37.50
3
9.38
33.33
18.75
9
28.13
 
 
2
0
0.00
0.00
0.00
4
12.50
100.00
25.00
4
12.50
 
 
3
8
25.00
66.67
50.00
4
12.50
33.33
25.00
12
37.50
 
 
4
2
6.25
28.57
12.50
5
15.63
71.43
31.25
7
21.88
 
 
Total
16
50.00
16
50.00
32
100.00

Table total_positive_autoab_count1 * DonorType

Cross-Tabular Freq Table

Frequency
Percent
Row Pct
Col Pct
Table of total_positive_autoab_count1 by DonorType
total_positive_autoab_count1 DonorType(DonorType)
1_No diabetes 3_T1D Total
0
16
50.00
66.67
100.00
8
25.00
33.33
50.00
24
75.00
 
 
1
0
0.00
0.00
0.00
4
12.50
100.00
25.00
4
12.50
 
 
2
0
0.00
0.00
0.00
1
3.13
100.00
6.25
1
3.13
 
 
3
0
0.00
0.00
0.00
3
9.38
100.00
18.75
3
9.38
 
 
Total
16
50.00
16
50.00
32
100.00

supplemental table 1: overall numbers for both studies

In [105]:
PROC sort data=duct_demo;
    by nPODCaseID;
RUN;

PROC sort data=cell_demo;
    by nPODCaseID;
RUN;


DATA overall;
merge duct_demo cell_demo;
by nPODCaseID;
run;

PROC freq data=overall;
    tables donortype;
RUN;


/*bring in INS+ status from study for main demo table*/

DATA overall;
    set overall;
    donortype1=donortype;
    if nPODCaseID=6052 then donortype1="T1D INS+";
    if nPODCaseID=6195 then donortype1="T1D INS+";
    if nPODCaseID=6209 then donortype1="T1D INS+";
    if nPODCaseID=6228 then donortype1="T1D INS+";
    if nPODCaseID=6243 then donortype1="T1D INS+";
    if nPODCaseID=6247 then donortype1="T1D INS+";
    if nPODCaseID=6265 then donortype1="T1D INS+";
    if nPODCaseID=6362 then donortype1="T1D INS+";
    if nPODCaseID=6371 then donortype1="T1D INS+";
    if nPODCaseID=6380 then donortype1="T1D INS+";
    if nPODCaseID=6396 then donortype1="T1D INS+";
    if nPODCaseID=6472 then donortype1="T1D INS+";
    if nPODCaseID=6062 then donortype1="T1D INS-";
    if nPODCaseID=6064 then donortype1="T1D INS-";
    if nPODCaseID=6079 then donortype1="T1D INS-";
    if nPODCaseID=6087 then donortype1="T1D INS-";
    if nPODCaseID=6089 then donortype1="T1D INS-";
    if nPODCaseID=6237 then donortype1="T1D INS-";
    if nPODCaseID=6360 then donortype1="T1D INS-";
run;

PROC freq data=overall;
    tables donortype donortype1;
RUN;

proc export data=overall
     outfile="&location\Data\overall.csv" 
     dbms=csv
     replace;
run; 


PROC Sort data=overall;
 by donortype1;
RUN;


PROC univariate data=overall;
    var oppc_ageR oppc_bmiR  oppc_c_peptideR1 hospitalization_stay_days transport_duration_hours diabetes_duration_yrs oppc_hba1cR oppc_hba1cR1;
RUN;

PROC means data=overall n mean std;
    var oppc_ageR oppc_bmiR  transport_duration_hours diabetes_duration_yrs;
    by donortype1;
RUN;

PROC means data=overall n median min max;
    var oppc_c_peptideR1 hospitalization_stay_days oppc_hba1cR oppc_hba1cR1 ;
    by donortype1;
RUN;

PROC freq data=overall ORDER=FORMATTED;
     format donortype1 $order.;
    tables oppc_gender*donortype1 oppc_ethnicity1*donortype1 cod4group*donortype1 total_positive_autoab_count1*donortype1 dr4dq0302_only*donortype1 dr0301dq0201_only*donortype1 dr4anddr0301*donortype1 dr1501dq0602*donortype1;
RUN;
Out[105]:
SAS Output

SAS Output

The SAS System

The FREQ Procedure

The FREQ Procedure

Table DonorType

One-Way Frequencies

DonorType
DonorType Frequency Percent Cumulative
Frequency
Cumulative
Percent
Autoab Pos 8 18.60 8 18.60
No diabetes 16 37.21 24 55.81
T1D 19 44.19 43 100.00

The SAS System

The FREQ Procedure

The FREQ Procedure

Table DonorType

One-Way Frequencies

DonorType
DonorType Frequency Percent Cumulative
Frequency
Cumulative
Percent
Autoab Pos 8 18.60 8 18.60
No diabetes 16 37.21 24 55.81
T1D 19 44.19 43 100.00

Table donortype1

One-Way Frequencies

donortype1 Frequency Percent Cumulative
Frequency
Cumulative
Percent
Autoab Pos 8 18.60 8 18.60
No diabetes 16 37.21 24 55.81
T1D INS+ 12 27.91 36 83.72
T1D INS- 7 16.28 43 100.00

The SAS System

The UNIVARIATE Procedure

Variable: oppc_ageR (oppc_ageR)

The UNIVARIATE Procedure

oppc_ageR

Moments

Moments
N 43 Sum Weights 43
Mean 13.9709302 Sum Observations 600.75
Std Deviation 5.84994213 Variance 34.2218229
Skewness 0.15199589 Kurtosis -0.9266621
Uncorrected SS 9830.3529 Corrected SS 1437.31656
Coeff Variation 41.872245 Std Error Mean 0.89210781

Basic Measures of Location and Variability

Basic Statistical Measures
Location Variability
Mean 13.97093 Std Deviation 5.84994
Median 13.00000 Variance 34.22182
Mode 13.00000 Range 20.50000
    Interquartile Range 7.95000

Tests For Location

Tests for Location: Mu0=0
Test Statistic p Value
Student's t t 15.66059 Pr > |t| <.0001
Sign M 21.5 Pr >= |M| <.0001
Signed Rank S 473 Pr >= |S| <.0001

Quantiles

Quantiles (Definition 5)
Level Quantile
100% Max 24.90
99% 24.90
95% 23.30
90% 22.10
75% Q3 18.20
50% Median 13.00
25% Q1 10.25
10% 5.00
5% 4.80
1% 4.40
0% Min 4.40

Extreme Observations

Extreme Observations
Lowest Highest
Value Obs Value Obs
4.4 1 22.1 7
4.7 18 23.0 3
4.8 43 23.3 15
5.0 27 24.0 30
5.0 17 24.9 32

The SAS System

The UNIVARIATE Procedure

Variable: oppc_bmiR (oppc_bmiR)

oppc_bmiR

Moments

Moments
N 43 Sum Weights 43
Mean 21.8060465 Sum Observations 937.66
Std Deviation 6.37695633 Variance 40.6655721
Skewness 2.4437793 Kurtosis 10.164027
Uncorrected SS 22154.6116 Corrected SS 1707.95403
Coeff Variation 29.2439821 Std Error Mean 0.97247672

Basic Measures of Location and Variability

Basic Statistical Measures
Location Variability
Mean 21.80605 Std Deviation 6.37696
Median 21.30000 Variance 40.66557
Mode 21.90000 Range 38.50000
    Interquartile Range 7.06000

Tests For Location

Tests for Location: Mu0=0
Test Statistic p Value
Student's t t 22.42321 Pr > |t| <.0001
Sign M 21.5 Pr >= |M| <.0001
Signed Rank S 473 Pr >= |S| <.0001

Quantiles

Quantiles (Definition 5)
Level Quantile
100% Max 51.40
99% 51.40
95% 28.50
90% 28.20
75% Q3 24.46
50% Median 21.30
25% Q1 17.40
10% 15.90
5% 14.80
1% 12.90
0% Min 12.90

Extreme Observations

Extreme Observations
Lowest Highest
Value Obs Value Obs
12.9 31 28.2 2
14.6 34 28.3 16
14.8 1 28.5 32
15.3 17 32.5 20
15.9 27 51.4 6

The SAS System

The UNIVARIATE Procedure

Variable: oppc_c_peptideR1

oppc_c_peptideR1

Moments

Moments
N 42 Sum Weights 42
Mean 4.25452381 Sum Observations 178.69
Std Deviation 6.41737588 Variance 41.1827132
Skewness 2.37601744 Kurtosis 6.77176579
Uncorrected SS 2448.7321 Corrected SS 1688.49124
Coeff Variation 150.836525 Std Error Mean 0.9902226

Basic Measures of Location and Variability

Basic Statistical Measures
Location Variability
Mean 4.254524 Std Deviation 6.41738
Median 1.800000 Variance 41.18271
Mode 0.050000 Range 31.09000
    Interquartile Range 5.37000

Tests For Location

Tests for Location: Mu0=0
Test Statistic p Value
Student's t t 4.296533 Pr > |t| 0.0001
Sign M 21 Pr >= |M| <.0001
Signed Rank S 451.5 Pr >= |S| <.0001

Quantiles

Quantiles (Definition 5)
Level Quantile
100% Max 31.11
99% 31.11
95% 16.59
90% 12.11
75% Q3 5.47
50% Median 1.80
25% Q1 0.10
10% 0.05
5% 0.05
1% 0.02
0% Min 0.02

Extreme Observations

Extreme Observations
Lowest Highest
Value Obs Value Obs
0.02 43 12.11 23
0.02 36 15.33 20
0.05 42 16.59 3
0.05 41 17.48 2
0.05 40 31.11 22

Missing Values

Missing Values
Missing
Value
Count Percent Of
All Obs Missing Obs
. 1 2.33 100.00

The SAS System

The UNIVARIATE Procedure

Variable: hospitalization_stay_days (hospitalization_stay_days)

hospitalization_stay_days

Moments

Moments
N 42 Sum Weights 42
Mean 4.42428571 Sum Observations 185.82
Std Deviation 2.74155034 Variance 7.51609826
Skewness 1.82167882 Kurtosis 3.61369854
Uncorrected SS 1130.2808 Corrected SS 308.160029
Coeff Variation 61.9659424 Std Error Mean 0.4230304

Basic Measures of Location and Variability

Basic Statistical Measures
Location Variability
Mean 4.424286 Std Deviation 2.74155
Median 3.700000 Variance 7.51610
Mode 1.840000 Range 11.95000
    Interquartile Range 2.55000

Tests For Location

Tests for Location: Mu0=0
Test Statistic p Value
Student's t t 10.45855 Pr > |t| <.0001
Sign M 21 Pr >= |M| <.0001
Signed Rank S 451.5 Pr >= |S| <.0001

Quantiles

Quantiles (Definition 5)
Level Quantile
100% Max 13.61
99% 13.61
95% 10.04
90% 7.42
75% Q3 5.24
50% Median 3.70
25% Q1 2.69
10% 1.84
5% 1.84
1% 1.66
0% Min 1.66

Extreme Observations

Extreme Observations
Lowest Highest
Value Obs Value Obs
1.66 10 7.42 9
1.71 30 7.76 32
1.84 26 10.04 28
1.84 25 12.78 35
1.84 11 13.61 14

Missing Values

Missing Values
Missing
Value
Count Percent Of
All Obs Missing Obs
. 1 2.33 100.00

The SAS System

The UNIVARIATE Procedure

Variable: transport_duration_hours (transport_duration_hours)

transport_duration_hours

Moments

Moments
N 42 Sum Weights 42
Mean 18.571 Sum Observations 779.982
Std Deviation 6.01789795 Variance 36.2150958
Skewness 1.69211671 Kurtosis 3.81105117
Uncorrected SS 15969.8646 Corrected SS 1484.81893
Coeff Variation 32.4048137 Std Error Mean 0.92858181

Basic Measures of Location and Variability

Basic Statistical Measures
Location Variability
Mean 18.57100 Std Deviation 6.01790
Median 17.85850 Variance 36.21510
Mode . Range 28.01600
    Interquartile Range 6.18300

Tests For Location

Tests for Location: Mu0=0
Test Statistic p Value
Student's t t 19.99931 Pr > |t| <.0001
Sign M 21 Pr >= |M| <.0001
Signed Rank S 451.5 Pr >= |S| <.0001

Quantiles

Quantiles (Definition 5)
Level Quantile
100% Max 38.8830
99% 38.8830
95% 32.0500
90% 22.5670
75% Q3 20.9330
50% Median 17.8585
25% Q1 14.7500
10% 12.2670
5% 11.1830
1% 10.8670
0% Min 10.8670

Extreme Observations

Extreme Observations
Lowest Highest
Value Obs Value Obs
10.867 43 22.567 18
11.150 41 22.983 30
11.183 24 32.050 14
12.133 38 36.583 36
12.267 42 38.883 12

Missing Values

Missing Values
Missing
Value
Count Percent Of
All Obs Missing Obs
. 1 2.33 100.00

The SAS System

The UNIVARIATE Procedure

Variable: diabetes_Duration_yrs

diabetes_Duration_yrs

Moments

Moments
N 19 Sum Weights 19
Mean 4.07105263 Sum Observations 77.35
Std Deviation 3.61921246 Variance 13.0986988
Skewness 0.60028958 Kurtosis -0.593801
Uncorrected SS 550.6725 Corrected SS 235.776579
Coeff Variation 88.9011464 Std Error Mean 0.83030428

Basic Measures of Location and Variability

Basic Statistical Measures
Location Variability
Mean 4.071053 Std Deviation 3.61921
Median 4.000000 Variance 13.09870
Mode 0.000000 Range 12.00000
    Interquartile Range 7.40000

Note: The mode displayed is the smallest of 2 modes with a count of 3.

Tests For Location

Tests for Location: Mu0=0
Test Statistic p Value
Student's t t 4.903085 Pr > |t| 0.0001
Sign M 8 Pr >= |M| <.0001
Signed Rank S 68 Pr >= |S| <.0001

Quantiles

Quantiles (Definition 5)
Level Quantile
100% Max 12.0
99% 12.0
95% 12.0
90% 9.0
75% Q3 8.0
50% Median 4.0
25% Q1 0.6
10% 0.0
5% 0.0
1% 0.0
0% Min 0.0

Extreme Observations

Extreme Observations
Lowest Highest
Value Obs Value Obs
0.00 34 8 31
0.00 32 8 39
0.00 28 8 41
0.25 27 9 38
0.60 30 12 42

Missing Values

Missing Values
Missing
Value
Count Percent Of
All Obs Missing Obs
. 24 55.81 100.00

The SAS System

The UNIVARIATE Procedure

Variable: oppc_HbA1cR

oppc_HbA1cR

Moments

Moments
N 29 Sum Weights 29
Mean 7.57586207 Sum Observations 219.7
Std Deviation 3.10007548 Variance 9.61046798
Skewness 0.98220391 Kurtosis -0.7111971
Uncorrected SS 1933.51 Corrected SS 269.093103
Coeff Variation 40.9204319 Std Error Mean 0.57566956

Basic Measures of Location and Variability

Basic Statistical Measures
Location Variability
Mean 7.575862 Std Deviation 3.10008
Median 5.600000 Variance 9.61047
Mode 5.500000 Range 8.50000
    Interquartile Range 4.60000

Note: The mode displayed is the smallest of 2 modes with a count of 4.

Tests For Location

Tests for Location: Mu0=0
Test Statistic p Value
Student's t t 13.16009 Pr > |t| <.0001
Sign M 14.5 Pr >= |M| <.0001
Signed Rank S 217.5 Pr >= |S| <.0001

Quantiles

Quantiles (Definition 5)
Level Quantile
100% Max 13.5
99% 13.5
95% 13.4
90% 13.3
75% Q3 10.0
50% Median 5.6
25% Q1 5.4
10% 5.2
5% 5.1
1% 5.0
0% Min 5.0

Extreme Observations

Extreme Observations
Lowest Highest
Value Obs Value Obs
5.0 3 12.4 37
5.1 21 13.1 29
5.2 13 13.3 28
5.3 19 13.4 35
5.3 18 13.5 34

Missing Values

Missing Values
Missing
Value
Count Percent Of
All Obs Missing Obs
. 14 32.56 100.00

The SAS System

The UNIVARIATE Procedure

Variable: oppc_hba1cR1

oppc_hba1cR1

Moments

Moments
N 29 Sum Weights 29
Mean 59.2901407 Sum Observations 1719.41408
Std Deviation 33.8880136 Variance 1148.39746
Skewness 0.98220391 Kurtosis -0.7111971
Uncorrected SS 134099.432 Corrected SS 32155.129
Coeff Variation 57.1562374 Std Error Mean 6.29284614

Basic Measures of Location and Variability

Basic Statistical Measures
Location Variability
Mean 59.29014 Std Deviation 33.88801
Median 37.69130 Variance 1148
Mode 36.59816 Range 92.91648
    Interquartile Range 50.28422

Note: The mode displayed is the smallest of 2 modes with a count of 4.

Tests For Location

Tests for Location: Mu0=0
Test Statistic p Value
Student's t t 9.421832 Pr > |t| <.0001
Sign M 14.5 Pr >= |M| <.0001
Signed Rank S 217.5 Pr >= |S| <.0001

Quantiles

Quantiles (Definition 5)
Level Quantile
100% Max 124.0490
99% 124.0490
95% 122.9558
90% 121.8627
75% Q3 85.7892
50% Median 37.6913
25% Q1 35.5050
10% 33.3188
5% 32.2256
1% 31.1325
0% Min 31.1325

Extreme Observations

Extreme Observations
Lowest Highest
Value Obs Value Obs
31.1325 3 112.024 37
32.2256 21 119.676 29
33.3188 13 121.863 28
34.4119 19 122.956 35
34.4119 18 124.049 34

Missing Values

Missing Values
Missing
Value
Count Percent Of
All Obs Missing Obs
. 14 32.56 100.00

The SAS System

The MEANS Procedure

The MEANS Procedure

donortype1=Autoab Pos

Summary statistics

Variable Label N Mean Std Dev
oppc_ageR
oppc_bmiR
transport_duration_hours
diabetes_Duration_yrs
oppc_ageR
oppc_bmiR
transport_duration_hours
 
8
8
8
0
15.7975000
24.9125000
18.5437500
.
7.9043148
11.4866926
2.4357926
.

donortype1=No diabetes

Summary statistics

Variable Label N Mean Std Dev
oppc_ageR
oppc_bmiR
transport_duration_hours
diabetes_Duration_yrs
oppc_ageR
oppc_bmiR
transport_duration_hours
 
16
16
16
0
12.7950000
21.2850000
19.7240000
.
5.2453319
4.7661445
7.1645742
.

donortype1=T1D INS+

Summary statistics

Variable Label N Mean Std Dev
oppc_ageR
oppc_bmiR
transport_duration_hours
diabetes_Duration_yrs
oppc_ageR
oppc_bmiR
transport_duration_hours
 
12
12
11
12
14.4708333
19.5583333
19.4407273
2.3208333
5.8147328
4.6406227
6.6148695
2.6074594

donortype1=T1D INS-

Summary statistics

Variable Label N Mean Std Dev
oppc_ageR
oppc_bmiR
transport_duration_hours
diabetes_Duration_yrs
oppc_ageR
oppc_bmiR
transport_duration_hours
 
7
7
7
7
13.7142857
23.3000000
14.6000000
7.0714286
5.2132615
2.8554042
3.9953397
3.1941166

The SAS System

The MEANS Procedure

The MEANS Procedure

donortype1=Autoab Pos

Summary statistics

Variable Label N Median Minimum Maximum
oppc_c_peptideR1
hospitalization_stay_days
oppc_HbA1cR
oppc_hba1cR1
 
hospitalization_stay_days
 
 
8
8
6
6
6.2200000
4.2300000
5.5500000
37.1447311
1.8400000
2.0400000
5.0000000
31.1324880
17.4800000
6.9000000
5.8000000
39.8775689

donortype1=No diabetes

Summary statistics

Variable Label N Median Minimum Maximum
oppc_c_peptideR1
hospitalization_stay_days
oppc_HbA1cR
oppc_hba1cR1
 
hospitalization_stay_days
 
 
16
16
13
13
4.2400000
3.7000000
5.4000000
35.5050284
1.1700000
1.6600000
5.1000000
32.2256231
31.1100000
13.6100000
6.3000000
45.3432444

donortype1=T1D INS+

Summary statistics

Variable Label N Median Minimum Maximum
oppc_c_peptideR1
hospitalization_stay_days
oppc_HbA1cR
oppc_hba1cR1
 
hospitalization_stay_days
 
 
12
11
7
7
0.1050000
4.0200000
13.1000000
119.6764320
0.0200000
1.7100000
9.5000000
80.3235680
0.4700000
12.7800000
13.5000000
124.0489725

donortype1=T1D INS-

Summary statistics

Variable Label N Median Minimum Maximum
oppc_c_peptideR1
hospitalization_stay_days
oppc_HbA1cR
oppc_hba1cR1
 
hospitalization_stay_days
 
 
6
7
3
3
0.0500000
2.7900000
10.4000000
90.1617840
0.0200000
1.9600000
10.2000000
87.9755138
0.0500000
4.2600000
12.4000000
112.0244862

The SAS System

The FREQ Procedure

The FREQ Procedure

Table oppc_Gender * donortype1

Cross-Tabular Freq Table

Frequency
Percent
Row Pct
Col Pct
Table of oppc_Gender by donortype1
oppc_Gender(oppc_Gender) donortype1
1_No diabetes 2_Autoab Pos T1D INS+ T1D INS- Total
Female
5
11.63
29.41
31.25
3
6.98
17.65
37.50
5
11.63
29.41
41.67
4
9.30
23.53
57.14
17
39.53
 
 
Male
11
25.58
42.31
68.75
5
11.63
19.23
62.50
7
16.28
26.92
58.33
3
6.98
11.54
42.86
26
60.47
 
 
Total
16
37.21
8
18.60
12
27.91
7
16.28
43
100.00

Table oppc_ethnicity1 * donortype1

Cross-Tabular Freq Table

Frequency
Percent
Row Pct
Col Pct
Table of oppc_ethnicity1 by donortype1
oppc_ethnicity1 donortype1
1_No diabetes 2_Autoab Pos T1D INS+ T1D INS- Total
African Am
5
11.63
50.00
31.25
2
4.65
20.00
25.00
2
4.65
20.00
16.67
1
2.33
10.00
14.29
10
23.26
 
 
Caucasian
11
25.58
34.38
68.75
5
11.63
15.63
62.50
10
23.26
31.25
83.33
6
13.95
18.75
85.71
32
74.42
 
 
Hispanic/Latino
0
0.00
0.00
0.00
1
2.33
100.00
12.50
0
0.00
0.00
0.00
0
0.00
0.00
0.00
1
2.33
 
 
Total
16
37.21
8
18.60
12
27.91
7
16.28
43
100.00

Table cod4group * donortype1

Cross-Tabular Freq Table

Frequency
Percent
Row Pct
Col Pct
Table of cod4group by donortype1
cod4group donortype1
1_No diabetes 2_Autoab Pos T1D INS+ T1D INS- Total
1
6
13.95
42.86
37.50
3
6.98
21.43
37.50
1
2.33
7.14
8.33
4
9.30
28.57
57.14
14
32.56
 
 
2
0
0.00
0.00
0.00
0
0.00
0.00
0.00
4
9.30
100.00
33.33
0
0.00
0.00
0.00
4
9.30
 
 
3
8
18.60
44.44
50.00
5
11.63
27.78
62.50
3
6.98
16.67
25.00
2
4.65
11.11
28.57
18
41.86
 
 
4
2
4.65
28.57
12.50
0
0.00
0.00
0.00
4
9.30
57.14
33.33
1
2.33
14.29
14.29
7
16.28
 
 
Total
16
37.21
8
18.60
12
27.91
7
16.28
43
100.00

Table total_positive_autoab_count1 * donortype1

Cross-Tabular Freq Table

Frequency
Percent
Row Pct
Col Pct
Table of total_positive_autoab_count1 by donortype1
total_positive_autoab_count1 donortype1
1_No diabetes 2_Autoab Pos T1D INS+ T1D INS- Total
0
16
37.21
64.00
100.00
0
0.00
0.00
0.00
5
11.63
20.00
41.67
4
9.30
16.00
57.14
25
58.14
 
 
1
0
0.00
0.00
0.00
3
6.98
37.50
37.50
3
6.98
37.50
25.00
2
4.65
25.00
28.57
8
18.60
 
 
2
0
0.00
0.00
0.00
5
11.63
83.33
62.50
1
2.33
16.67
8.33
0
0.00
0.00
0.00
6
13.95
 
 
3
0
0.00
0.00
0.00
0
0.00
0.00
0.00
3
6.98
75.00
25.00
1
2.33
25.00
14.29
4
9.30
 
 
Total
16
37.21
8
18.60
12
27.91
7
16.28
43
100.00

Table dr4dq0302_only * donortype1

Cross-Tabular Freq Table

Frequency
Percent
Row Pct
Col Pct
Table of dr4dq0302_only by donortype1
dr4dq0302_only donortype1
1_No diabetes 2_Autoab Pos T1D INS+ T1D INS- Total
0
11
26.19
35.48
68.75
7
16.67
22.58
87.50
9
21.43
29.03
81.82
4
9.52
12.90
57.14
31
73.81
 
 
1
5
11.90
45.45
31.25
1
2.38
9.09
12.50
2
4.76
18.18
18.18
3
7.14
27.27
42.86
11
26.19
 
 
Total
16
38.10
8
19.05
11
26.19
7
16.67
42
100.00
Frequency Missing = 1

Table dr0301dq0201_only * donortype1

Cross-Tabular Freq Table

Frequency
Percent
Row Pct
Col Pct
Table of dr0301dq0201_only by donortype1
dr0301dq0201_only donortype1
1_No diabetes 2_Autoab Pos T1D INS+ T1D INS- Total
0
13
30.95
43.33
81.25
5
11.90
16.67
62.50
6
14.29
20.00
54.55
6
14.29
20.00
85.71
30
71.43
 
 
1
3
7.14
25.00
18.75
3
7.14
25.00
37.50
5
11.90
41.67
45.45
1
2.38
8.33
14.29
12
28.57
 
 
Total
16
38.10
8
19.05
11
26.19
7
16.67
42
100.00
Frequency Missing = 1

Table dr4anddr0301 * donortype1

Cross-Tabular Freq Table

Frequency
Percent
Row Pct
Col Pct
Table of dr4anddr0301 by donortype1
dr4anddr0301 donortype1
1_No diabetes 2_Autoab Pos T1D INS+ T1D INS- Total
0
16
38.10
44.44
100.00
7
16.67
19.44
87.50
8
19.05
22.22
72.73
5
11.90
13.89
71.43
36
85.71
 
 
1
0
0.00
0.00
0.00
1
2.38
16.67
12.50
3
7.14
50.00
27.27
2
4.76
33.33
28.57
6
14.29
 
 
Total
16
38.10
8
19.05
11
26.19
7
16.67
42
100.00
Frequency Missing = 1

Table dr1501dq0602 * donortype1

Cross-Tabular Freq Table

Frequency
Percent
Row Pct
Col Pct
Table of dr1501dq0602 by donortype1
dr1501dq0602 donortype1
1_No diabetes 2_Autoab Pos T1D INS+ T1D INS- Total
0
14
33.33
36.84
87.50
7
16.67
18.42
87.50
10
23.81
26.32
90.91
7
16.67
18.42
100.00
38
90.48
 
 
1
2
4.76
50.00
12.50
1
2.38
25.00
12.50
1
2.38
25.00
9.09
0
0.00
0.00
0.00
4
9.52
 
 
Total
16
38.10
8
19.05
11
26.19
7
16.67
42
100.00
Frequency Missing = 1

supplemental figures 1-2

supplemental figure 2:pancreas weight differences

In [106]:
/*for supplemental figure 1 - analyze all nPOD data*/

DATA panc;
    set clinical1;
    if oppc_ageR<=1 then age_group=0;                     /*developmental and neonates*/
    if oppc_ageR>1 and oppc_ageR<=12 then age_group=1;   /*child*/
    if oppc_ageR>12 and oppc_ageR<=18 then age_group=2;  /*adolescent*/
    if oppc_ageR>18 then age_group=3;                   /*adult*/

    
    if donortype^="No diabetes" and donortype^="Autoab Pos" and donortype^="T1D" then delete;
    if donortype="No diabetes" then donor_group=1;
    if donortype="Autoab Pos" then donor_group=2;
    if donortype="T1D" then donor_group=3;

    if pancreas_received_intact="FALSE" then delete;
    if whole_pancreas_g=. then delete;
    weight_g=oppc_weightR*1000;
    relative=whole_pancreas_g/weight_g*100;
    
    /*bring in finding from study regarding insulin positivity (main data)*/
    insulin_positive="INS+";
    if npodcaseid=6062 then insulin_positive="INS-";
    if npodcaseid=6079 then insulin_positive="INS-";
    if npodcaseid=6087 then insulin_positive="INS-";
    if npodcaseid=6360 then insulin_positive="INS-";
    if npodcaseid=6064 then insulin_positive="INS-";
    if npodcaseid=6089 then insulin_positive="INS-";
    if npodcaseid=6237 then insulin_positive="INS-";

RUN;

proc freq data=panc;
    tables donortype donor_group;
run;

proc sort data=panc; by age_group; run;

proc means data=panc n mean std median min max;
    class age_group donortype;
var whole_pancreas_g;

run;

/*for supplemental figure 2a - nPOD collection*/
proc export data=panc
     outfile="&location\Data\panc_all.csv" 
     dbms=csv
     replace;
run; 

/*for supplemental figure 2a - this study*/
PROC sort data=panc;
    by npodcaseid;
run;
PROC sort data=overall;
    by npodcaseid;
RUN;

DATA panc_limited;
    merge panc (in=a) overall (in=b);
    by npodcaseid;
    if a and b;
RUN;

proc export data=panc_limited
     outfile="&location\Data\panc_limited.csv" 
     dbms=csv
     replace;
run; 


/*for supplemental figure 2B - nPOD collection*/
DATA panc1;
    set panc;
    if diabetes_duration_yrs=. then delete;
RUN;

proc export data=panc1
     outfile="&location\Data\panc_all_disease_duration.csv" 
     dbms=csv
     replace;
run;

/*for supplemental figure 2B - this study*/


DATA panc_limited_disease_duration;
    set panc_limited;
    if diabetes_duration_yrs=. then delete;
RUN;

proc export data=panc_limited_disease_duration
     outfile="&location\Data\panc_limited_disease_duration.csv" 
     dbms=csv
     replace;
run;
Out[106]:
SAS Output

SAS Output

The SAS System

The FREQ Procedure

The FREQ Procedure

Table DonorType

One-Way Frequencies

DonorType
DonorType Frequency Percent Cumulative
Frequency
Cumulative
Percent
Autoab Pos 32 10.29 32 10.29
No diabetes 167 53.70 199 63.99
T1D 112 36.01 311 100.00

Table donor_group

One-Way Frequencies

donor_group Frequency Percent Cumulative
Frequency
Cumulative
Percent
1 167 53.70 167 53.70
2 32 10.29 199 63.99
3 112 36.01 311 100.00

The SAS System

The MEANS Procedure

The MEANS Procedure

Summary statistics

Analysis Variable : whole_pancreas_g whole_pancreas_g
age_group DonorType N Obs N Mean Std Dev Median Minimum Maximum
0 Autoab Pos 1 1 3.1200000 . 3.1200000 3.1200000 3.1200000
  No diabetes 28 28 4.4485714 2.5754607 4.0200000 0.7300000 10.4300000
1 Autoab Pos 3 3 30.3666667 12.1977758 28.6800000 19.1000000 43.3200000
  No diabetes 42 42 28.9128571 11.6739289 26.9000000 10.4700000 53.4100000
  T1D 10 10 21.8040000 10.2673638 19.4150000 10.3000000 41.1000000
2 Autoab Pos 1 1 111.0700000 . 111.0700000 111.0700000 111.0700000
  No diabetes 35 35 61.6985714 15.1341560 60.9300000 37.4000000 97.9900000
  T1D 14 14 37.6450000 10.8483609 33.7500000 22.7600000 60.0000000
3 Autoab Pos 27 27 73.1059259 20.9989125 71.8000000 25.0000000 110.3000000
  No diabetes 62 62 79.2083871 18.3409735 79.3500000 45.6000000 139.0000000
  T1D 88 88 43.2147727 17.9015551 38.8000000 14.2600000 117.4000000
In [107]:
#suppl fig2a 
temp<-import('panc_all.csv')
temp1<-import('panc_limited.csv')


#smoothing fits that were not used
#method="lm", formula = y ~ x + I(x^2)
#method="loess", span=0.7
#method="lm", formula = y ~ poly(x, 2)

#colors
#use #E7298A(pink) to match color palette below.  This is for T1D with no insulin containing islets, and we will use the purple color below as T1D with ICIs.


p <- ggplot(temp, aes(donor_group, relative))
p <- ggplot(temp, aes(oppc_ageR, relative))

supp_fig2a_all<-p  +  
geom_jitter(data=temp, aes(color = DonorType, fill = DonorType), shape=21, width=2, alpha = 0.2, size=3) +
geom_jitter(data=temp1, aes(fill=DonorType),  shape=21, width=2,  alpha = 1, size=4) +
geom_smooth(aes(group = DonorType, color = DonorType), se = TRUE, alpha=0.2, level=0.95, method = "gam", formula = y ~ s(x, k = 3)) + #can specify level=0.95 for 95% confidence interval when se=TRUE, also a family="symmetric" to help control outliers when using LOESS
scale_color_manual(values =c("#D95F02", "#1B9E77", "#666666")) + #comment this line out if you want to use R's auto-color palette
scale_fill_manual(values=c("No diabetes" = "#1B9E77", "Autoab Pos" = "#D95F02", "T1D" = "#666666")) +  #comment this line out if you want to use R's auto-color palette

theme_few() +
  ylab("Pancreas weight\n(% of body weight)\n") +
  xlab("Age(years)") +
  labs(color = "Donor Group") +
  # replace none with the following to add the legend back into the figure: c(.785,.90)  
  theme(legend.position = "none",legend.text=element_text(size=18, face="bold", family="Arial"), legend.title=element_text(size=20, face="bold", family="Arial"),
        axis.text=element_text(size=20, color="black", family="Arial"), axis.title=element_text(size=20, face="bold", family="Arial"), axis.ticks=element_line(color="black"),
        panel.border = element_rect(color = "black")) +
  geom_vline(xintercept = c(1,12, 18), linetype = "longdash", color = "black", size=0.5) +
  #annotate(geom = "text", x = 4, y = .17, label = "\u22651", color = "black", size=5, family="Arial") +
  annotate(geom = "text", x = 7, y = .25, label = "*", color = "black", size=8, family="Arial") +
  #annotate(geom = "text", x = 16, y = 3, label = "3", color = "black", size=5, family="Arial") +
  #annotate(geom = "text", x = 45, y = .25, label = "**", color = "black", size=8, family="Arial") +
   coord_cartesian(xlim = c(0, 70))+
scale_y_continuous (limits=c(0.00,.25), breaks=c(0,0.10, 0.20))+
scale_x_continuous(breaks=c(0,1,12,18,20,40,60), labels=c("",1,12,"",20,40,60))

supp_fig2a_all

save_plot("supp_fig2a_all.tiff", supp_fig2a_all, dpi=300, base_aspect_ratio=1.5)
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In [108]:
#supp figure 2b 
temp<-import('panc_all_disease_duration.csv')
temp1<-import('panc_limited_disease_duration.csv')

#smoothing fits that were not used
#method="lm", formula = y ~ x + I(x^2)
#method="loess", span=0.7
#method="lm", formula = y ~ poly(x, 2)
#method = "gam", formula = y ~ s(x, k = 3)) 
#colors
#use #E7298A(pink) to match color palette below.  This is for T1D with no insulin containing islets, and we will use the purple color below as T1D with ICIs.


temp %<>% mutate(age_group = ifelse(age_group == "0", "Dev./Neonates",
                                       ifelse(age_group == "1", "Children",
                                              ifelse(age_group == "2", "Adolescents",
                                                    "Adults"))))

temp <- within(temp,age_group <- factor(age_group,
                                            levels=rev(c("Adults",
                                                     "Adolescents",
                                                     "Children",
                                                        "Dev./Neonates"))))

p <- ggplot(temp, aes(donor_group, relative))
p <- ggplot(temp, aes(diabetes_Duration_yrs, relative))

supp_fig2b_all<-p  +  
geom_jitter(aes(color="G", fill="G"), shape=21, alpha = .2, size=3) +
geom_jitter(data=temp1, aes(fill=insulin_positive), shape=21, alpha = 1, size=4) +
geom_smooth(se = TRUE, color="black", alpha=0.2, level=0.95, method="gam", formula = y ~ s(x, k = 3)) + #can specify level=0.95 for 95% confidence interval when se=TRUE, also a family="symmetric" to help control outliers when using LOESS
scale_color_manual(values=c("#666666",  "#E7298A", "#7570B3"))+ 
scale_fill_manual(values=c("#666666",  "#E7298A", "#7570B3"))+

#scale_color_brewer(palette= "PRGn", type="seq")+ #simple way to select color palette
#scale_fill_brewer(palette="PRGn", type="seq")+

#scale_color_manual(values =c("#141204", "#244F26", "#8F3985", "#B3B3B3")) + #custom colors
#  scale_fill_manual(values=c("dev" = "141204", "child" = "#244F26", "adol" = "#8F3985", "adult" = "#B3B3B3")) +  #custom colors
  theme_few() +
  ylab("Pancreas weight\n(% of body weight)\n") +
  xlab("T1D Duration (years)") +
  labs(color = "Donor Group") +
  # replace none with the following to add the legend back into the figure: c(.785,.90)  
  theme(legend.position = "none",legend.text=element_text(size=14, family="Arial"), legend.title=element_blank(),
        axis.text=element_text(size=20, color="black", family="Arial"),  axis.title=element_text(size=20, face="bold", family="Arial"), axis.ticks=element_line(color="black"),
        panel.border = element_rect(color = "black")) +
  #geom_vline(xintercept = c(12, 20), linetype = "longdash", color = "black", size=0.5) 
# annotate(geom = "text", x = 25, y = .25, label = "*", color = "black", size=8, family="Arial") +
 # annotate(geom = "text", x = 16, y = .17, label = "Youth", color = "black", size=6.5, family="Arial") +
 # annotate(geom = "text", x = 23, y = .17, label = "Adults", color = "black", size=6.5, family="Arial") +
  coord_cartesian(xlim = c(0, 55))+
scale_y_continuous (limits=c(0.00,.25), breaks=c(0,0.10, 0.20)) +
scale_x_continuous (limits=c(0,60), breaks=c(0,5,10,20,40,55))

#for customizing legend within plot
#guides(colour = guide_legend(nrow = 1))
#legend.position = c(0.5,0.96)

supp_fig2b_all

save_plot("supp_fig2b_all.tiff", supp_fig2b_all, dpi=300, base_aspect_ratio=1.5)
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In [109]:
save_plot("supp_fig2.tiff", plot_grid(supp_fig2a_all, supp_fig2b_all, labels = "AUTO", label_size=20), dpi=300, base_aspect_ratio=1/.30)
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statistical analysis for supp fig2

In [110]:
data children;
set panc_limited;
if age_group^=1 then delete;
run;

proc mixed data=children;
class donortype npodCaseID oppc_gender ;
model relative=donortype /solution ddfm = kenwardroger;
random int/ subject=nPODCaseid;
lsmeans DonorType/adjust=tukey cl pdiff alpha=0.05;
run;

proc sort data=children; by donortype; run;
proc means data=children n mean std median min max;
var relative;
by donortype;
run;


data adult;
set panc_limited;
if age_group^=3 then delete;
run;


proc mixed data=adult;
class donortype npodCaseID oppc_gender;
model relative=donortype /solution ddfm = kenwardroger;
random int/ subject=nPODCaseid;
lsmeans DonorType/adjust=tukey cl pdiff alpha=0.05;
run;

proc sort data=adult; by donortype; run;
proc means data=adult n mean std median min max;
var relative;
by donortype;
run;



/*did not analyze either of these age groups due to only having 1 donor in a group*/
data neo;
set panc_limited;
if age_group^=0 then delete;
run;

data adol;
set panc_limited;
if age_group^=2 then delete;
run;

/*tested disease duration differences*/
data t1d;
    set panc_limited;
    if diabetes_duration_yrs="." then delete;
    if relative="." then delete;
    if diabetes_duration_yrs<=5 then disease_bin=0;                     /*new onset*/
    if diabetes_duration_yrs>5 and diabetes_duration_yrs<=10 then disease_bin=1;   /*new onset +*/
    if diabetes_duration_yrs>10 and diabetes_duration_yrs<=20 then disease_bin=2;  /*long duration - */
    if diabetes_duration_yrs>20 then disease_bin=3;   /*long duration*/
run;

proc freq data=t1d;
tables disease_bin;
run;

proc mixed data=t1d;
class npodCaseID oppc_gender disease_bin;
model relative=disease_bin /solution ddfm = kenwardroger;
random int/ subject=nPODCaseid;
lsmeans disease_bin/adjust=tukey cl pdiff alpha=0.05;
run;


proc mixed data=t1d;
class npodCaseID oppc_gender disease_bin insulin_positive;
model relative=diabetes_duration_yrs|insulin_positive /solution ddfm = kenwardroger;
random int/ subject=nPODCaseid;
     lsmeans insulin_positive/adjust=tukey cl pdiff alpha=0.05;
run;

proc mixed data=t1d;
class npodCaseID oppc_gender disease_bin insulin_positive;
model relative=diabetes_duration_yrs insulin_positive /solution ddfm = kenwardroger;
random int/ subject=nPODCaseid;
     lsmeans insulin_positive/adjust=tukey cl pdiff alpha=0.05;
run;
Out[110]:
SAS Output

SAS Output

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CHILDREN
Dependent Variable relative
Covariance Structure Variance Components
Subject Effect nPODCaseID
Estimation Method REML
Residual Variance Method Profile
Fixed Effects SE Method Kenward-Roger
Degrees of Freedom Method Kenward-Roger

Class Level Information

Class Level Information
Class Levels Values
DonorType 3 Autoab Pos No diabetes T1D
nPODCaseID 17 6052 6062 6079 6209 6265 6278 6293 6318 6334 6347 6357 6360 6380 6382 6385 6421 6434
oppc_Gender 2 Female Male

Dimensions

Dimensions
Covariance Parameters 2
Columns in X 4
Columns in Z per Subject 1
Subjects 17
Max Obs per Subject 1

Number of Observations

Number of Observations
Number of Observations Read 17
Number of Observations Used 17
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 -55.96346384  
1 1 -55.96346384 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Intercept nPODCaseID 5.887E-7
Residual   0.000767

Fit Statistics

Fit Statistics
-2 Res Log Likelihood -56.0
AIC (Smaller is Better) -52.0
AICC (Smaller is Better) -50.9
BIC (Smaller is Better) -50.3

Solution for Fixed Effects

Solution for Fixed Effects
Effect DonorType Estimate Standard
Error
DF t Value Pr > |t|
Intercept   0.06557 0.01047 14 6.26 <.0001
DonorType Autoab Pos 0.05666 0.02221 14 2.55 0.0231
DonorType No diabetes 0.03052 0.01434 14 2.13 0.0515
DonorType T1D 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
DonorType 2 14 4.14 0.0387

Least Squares Means

Least Squares Means
Effect DonorType Estimate Standard
Error
DF t Value Pr > |t| Alpha Lower Upper
DonorType Autoab Pos 0.1222 0.01959 14 6.24 <.0001 0.05 0.08022 0.1643
DonorType No diabetes 0.09609 0.009795 14 9.81 <.0001 0.05 0.07508 0.1171
DonorType T1D 0.06557 0.01047 14 6.26 <.0001 0.05 0.04311 0.08803

Differences of Least Squares Means

Differences of Least Squares Means
Effect DonorType DonorType Estimate Standard
Error
DF t Value Pr > |t| Adjustment Adj P Alpha Lower Upper Adj Lower Adj Upper
DonorType Autoab Pos No diabetes 0.02615 0.02190 14 1.19 0.2524 Tukey-Kramer 0.4760 0.05 -0.02083 0.07312 -0.03118 0.08347
DonorType Autoab Pos T1D 0.05666 0.02221 14 2.55 0.0231 Tukey-Kramer 0.0565 0.05 0.009021 0.1043 -0.00147 0.1148
DonorType No diabetes T1D 0.03052 0.01434 14 2.13 0.0515 Tukey-Kramer 0.1198 0.05 -0.00023 0.06127 -0.00701 0.06805

The SAS System

The MEANS Procedure

The MEANS Procedure

DonorType=Autoab Pos

Summary statistics

Analysis Variable : relative
N Mean Std Dev Median Minimum Maximum
2 0.1222365 0.0073189 0.1222365 0.1170612 0.1274118

DonorType=No diabetes

Summary statistics

Analysis Variable : relative
N Mean Std Dev Median Minimum Maximum
8 0.0960913 0.0303781 0.0890162 0.0641221 0.1607333

DonorType=T1D

Summary statistics

Analysis Variable : relative
N Mean Std Dev Median Minimum Maximum
7 0.0655729 0.0265593 0.0689535 0.0379167 0.1112338

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.ADULT
Dependent Variable relative
Covariance Structure Variance Components
Subject Effect nPODCaseID
Estimation Method REML
Residual Variance Method Profile
Fixed Effects SE Method Kenward-Roger
Degrees of Freedom Method Kenward-Roger

Class Level Information

Class Level Information
Class Levels Values
DonorType 3 Autoab Pos No diabetes T1D
nPODCaseID 9 6064 6195 6197 6238 6247 6267 6362 6429 6450
oppc_Gender 2 Female Male

Dimensions

Dimensions
Covariance Parameters 2
Columns in X 4
Columns in Z per Subject 1
Subjects 9
Max Obs per Subject 1

Number of Observations

Number of Observations
Number of Observations Read 9
Number of Observations Used 9
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 -28.64310278  
1 1 -28.64310278 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Intercept nPODCaseID 9.706E-8
Residual   0.000311

Fit Statistics

Fit Statistics
-2 Res Log Likelihood -28.6
AIC (Smaller is Better) -24.6
AICC (Smaller is Better) -20.6
BIC (Smaller is Better) -24.2

Solution for Fixed Effects

Solution for Fixed Effects
Effect DonorType Estimate Standard
Error
DF t Value Pr > |t|
Intercept   0.06321 0.008826 6 7.16 0.0004
DonorType Autoab Pos 0.02509 0.01248 6 2.01 0.0911
DonorType No diabetes 0.05993 0.01974 6 3.04 0.0229
DonorType T1D 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
DonorType 2 6 5.22 0.0485

Least Squares Means

Least Squares Means
Effect DonorType Estimate Standard
Error
DF t Value Pr > |t| Alpha Lower Upper
DonorType Autoab Pos 0.08830 0.008826 6 10.01 <.0001 0.05 0.06671 0.1099
DonorType No diabetes 0.1231 0.01765 6 6.98 0.0004 0.05 0.07996 0.1663
DonorType T1D 0.06321 0.008826 6 7.16 0.0004 0.05 0.04162 0.08481

Differences of Least Squares Means

Differences of Least Squares Means
Effect DonorType DonorType Estimate Standard
Error
DF t Value Pr > |t| Adjustment Adj P Alpha Lower Upper Adj Lower Adj Upper
DonorType Autoab Pos No diabetes -0.03484 0.01974 6 -1.77 0.1279 Tukey-Kramer 0.2585 0.05 -0.08314 0.01345 -0.09540 0.02571
DonorType Autoab Pos T1D 0.02509 0.01248 6 2.01 0.0911 Tukey-Kramer 0.1905 0.05 -0.00545 0.05563 -0.01321 0.06339
DonorType No diabetes T1D 0.05993 0.01974 6 3.04 0.0229 Tukey-Kramer 0.0520 0.05 0.01164 0.1082 -0.00062 0.1205

The SAS System

The MEANS Procedure

The MEANS Procedure

DonorType=Autoab Pos

Summary statistics

Analysis Variable : relative
N Mean Std Dev Median Minimum Maximum
4 0.0883048 0.0173262 0.0822252 0.0749844 0.1137842

DonorType=No diabetes

Summary statistics

Analysis Variable : relative
N Mean Std Dev Median Minimum Maximum
1 0.1231494 . 0.1231494 0.1231494 0.1231494

DonorType=T1D

Summary statistics

Analysis Variable : relative
N Mean Std Dev Median Minimum Maximum
4 0.0632146 0.0179717 0.0663931 0.0397333 0.0803390

The SAS System

The FREQ Procedure

The FREQ Procedure

Table disease_bin

One-Way Frequencies

disease_bin Frequency Percent Cumulative
Frequency
Cumulative
Percent
0 11 64.71 11 64.71
1 5 29.41 16 94.12
2 1 5.88 17 100.00

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.T1D
Dependent Variable relative
Covariance Structure Variance Components
Subject Effect nPODCaseID
Estimation Method REML
Residual Variance Method Profile
Fixed Effects SE Method Kenward-Roger
Degrees of Freedom Method Kenward-Roger

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 17 6052 6062 6064 6079 6087 6089 6195 6209 6237 6243 6247 6265 6360 6362 6371 6380 6396
oppc_Gender 2 Female Male
disease_bin 3 0 1 2

Dimensions

Dimensions
Covariance Parameters 2
Columns in X 4
Columns in Z per Subject 1
Subjects 17
Max Obs per Subject 1

Number of Observations

Number of Observations
Number of Observations Read 17
Number of Observations Used 17
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 -64.54648402  
1 1 -64.54648402 0.00000000

Convergence Status

Convergence criteria met but final hessian is not positive definite.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Intercept nPODCaseID 1.913E-7
Residual   0.000437

Fit Statistics

Fit Statistics
-2 Res Log Likelihood -64.5
AIC (Smaller is Better) -60.5
AICC (Smaller is Better) -59.5
BIC (Smaller is Better) -58.9

Solution for Fixed Effects

Solution for Fixed Effects
Effect disease_bin Estimate Standard
Error
DF t Value Pr > |t|
Intercept   0.04335 0.02091 14 2.07 0.0572
disease_bin 0 0.02105 0.02184 14 0.96 0.3516
disease_bin 1 0.02477 0.02291 14 1.08 0.2978
disease_bin 2 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
disease_bin 2 14 0.59 0.5700

Least Squares Means

Least Squares Means
Effect disease_bin Estimate Standard
Error
DF t Value Pr > |t| Alpha Lower Upper
disease_bin 0 0.06440 0.006306 14 10.21 <.0001 0.05 0.05087 0.07792
disease_bin 1 0.06812 0.009353 14 7.28 <.0001 0.05 0.04806 0.08818
disease_bin 2 0.04335 0.02091 14 2.07 0.0572 0.05 -0.00151 0.08820

Differences of Least Squares Means

Differences of Least Squares Means
Effect disease_bin _disease_bin Estimate Standard
Error
DF t Value Pr > |t| Adjustment Adj P Alpha Lower Upper Adj Lower Adj Upper
disease_bin 0 1 -0.00373 0.01128 14 -0.33 0.7461 Tukey-Kramer 0.9419 0.05 -0.02792 0.02047 -0.03325 0.02580
disease_bin 0 2 0.02105 0.02184 14 0.96 0.3516 Tukey-Kramer 0.6108 0.05 -0.02580 0.06790 -0.03612 0.07822
disease_bin 1 2 0.02477 0.02291 14 1.08 0.2978 Tukey-Kramer 0.5406 0.05 -0.02437 0.07391 -0.03519 0.08474

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.T1D
Dependent Variable relative
Covariance Structure Variance Components
Subject Effect nPODCaseID
Estimation Method REML
Residual Variance Method Profile
Fixed Effects SE Method Kenward-Roger
Degrees of Freedom Method Kenward-Roger

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 17 6052 6062 6064 6079 6087 6089 6195 6209 6237 6243 6247 6265 6360 6362 6371 6380 6396
oppc_Gender 2 Female Male
disease_bin 3 0 1 2
insulin_positive 2 INS+ INS-

Dimensions

Dimensions
Covariance Parameters 2
Columns in X 6
Columns in Z per Subject 1
Subjects 17
Max Obs per Subject 1

Number of Observations

Number of Observations
Number of Observations Read 17
Number of Observations Used 17
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 -50.11185805  
1 1 -50.11185805 0.00000000

Convergence Status

Convergence criteria met but final hessian is not positive definite.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Intercept nPODCaseID 2.225E-7
Residual   0.000472

Fit Statistics

Fit Statistics
-2 Res Log Likelihood -50.1
AIC (Smaller is Better) -46.1
AICC (Smaller is Better) -44.9
BIC (Smaller is Better) -44.4

Solution for Fixed Effects

Solution for Fixed Effects
Effect insulin_positive Estimate Standard
Error
DF t Value Pr > |t|
Intercept   0.06420 0.02128 13 3.02 0.0099
diabetes_Duration_yr   -0.00010 0.002776 13 -0.04 0.9717
insulin_positive INS+ 0.007094 0.02325 13 0.31 0.7651
insulin_positive INS- 0 . . . .
diabetes_*insulin_po INS+ -0.00263 0.003847 13 -0.68 0.5069
diabetes_*insulin_po INS- 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
diabetes_Duration_yr 1 13 0.54 0.4755
insulin_positive 1 13 0.09 0.7651
diabetes_*insulin_po 1 13 0.47 0.5069

Least Squares Means

Least Squares Means
Effect insulin_positive Estimate Standard
Error
DF t Value Pr > |t| Alpha Lower Upper
insulin_positive INS+ 0.05953 0.008579 13 6.94 <.0001 0.05 0.04100 0.07806
insulin_positive INS- 0.06376 0.01122 13 5.68 <.0001 0.05 0.03952 0.08801

Differences of Least Squares Means

Differences of Least Squares Means
Effect insulin_positive _insulin_positive Estimate Standard
Error
DF t Value Pr > |t| Adjustment Adj P Alpha Lower Upper Adj Lower Adj Upper
insulin_positive INS+ INS- -0.00424 0.01413 13 -0.30 0.7691 Tukey-Kramer 0.7691 0.05 -0.03476 0.02628 -0.03475 0.02628

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.T1D
Dependent Variable relative
Covariance Structure Variance Components
Subject Effect nPODCaseID
Estimation Method REML
Residual Variance Method Profile
Fixed Effects SE Method Kenward-Roger
Degrees of Freedom Method Kenward-Roger

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 17 6052 6062 6064 6079 6087 6089 6195 6209 6237 6243 6247 6265 6360 6362 6371 6380 6396
oppc_Gender 2 Female Male
disease_bin 3 0 1 2
insulin_positive 2 INS+ INS-

Dimensions

Dimensions
Covariance Parameters 2
Columns in X 4
Columns in Z per Subject 1
Subjects 17
Max Obs per Subject 1

Number of Observations

Number of Observations
Number of Observations Read 17
Number of Observations Used 17
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 -58.93945442  
1 1 -58.93945442 0.00000000

Convergence Status

Convergence criteria met but final hessian is not positive definite.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Intercept nPODCaseID 2.059E-7
Residual   0.000454

Fit Statistics

Fit Statistics
-2 Res Log Likelihood -58.9
AIC (Smaller is Better) -54.9
AICC (Smaller is Better) -53.8
BIC (Smaller is Better) -53.3

Solution for Fixed Effects

Solution for Fixed Effects
Effect insulin_positive Estimate Standard
Error
DF t Value Pr > |t|
Intercept   0.07387 0.01557 14 4.74 0.0003
diabetes_Duration_yr   -0.00147 0.001885 14 -0.78 0.4490
insulin_positive INS+ -0.00558 0.01372 14 -0.41 0.6905
insulin_positive INS- 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
diabetes_Duration_yr 1 14 0.61 0.4490
insulin_positive 1 14 0.17 0.6905

Least Squares Means

Least Squares Means
Effect insulin_positive Estimate Standard
Error
DF t Value Pr > |t| Alpha Lower Upper
insulin_positive INS+ 0.06196 0.007656 14 8.09 <.0001 0.05 0.04554 0.07838
insulin_positive INS- 0.06753 0.009583 14 7.05 <.0001 0.05 0.04698 0.08809

Differences of Least Squares Means

Differences of Least Squares Means
Effect insulin_positive _insulin_positive Estimate Standard
Error
DF t Value Pr > |t| Adjustment Adj P Alpha Lower Upper Adj Lower Adj Upper
insulin_positive INS+ INS- -0.00558 0.01372 14 -0.41 0.6905 Tukey-Kramer 0.6905 0.05 -0.03500 0.02385 -0.03500 0.02385

supplemental figure 1

In [111]:
dataset <- import("cell3.csv")

dataset %<>% mutate(pancreas_region = ifelse(region == "PH", "Head",
                                             ifelse(region == "PB", "Body",
                                                    "Tail")),
                    donor_range = ifelse(donorgroup == "No diabetes", "No diabetes",
                                       ifelse(donorgroup == "Autoab Pos", "AAb+",
                                              ifelse(donorgroup == "Ins. pos. T1D", "T1D INS+",
                                                    "T1D INS-"))))
dataset$nPODCaseID <- as.character(dataset$nPODCaseID)


#order the variables
dataset <- within(dataset,pancreas_region <- factor(pancreas_region,
                                            levels=rev(c("Tail",
                                                     "Body",
                                                     "Head"))))

dataset <- within(dataset,donor_range <- factor(donor_range,
                                            levels=rev(c("T1D INS-",
                                                     "T1D INS+",
                                                     "AAb+",
                                                        "No diabetes"))))

colnames(dataset)

#need to calculate means at each level of each group, to plot simple effects 
meandataset <- ddply(dataset,.(donor_range,pancreas_region),summarise, val = mean(percent_endocrine_area))
meandataset

p <- ggplot(dataset, aes(pancreas_region, percent_endocrine_area))


suppfig1_1<-p + geom_jitter(aes(color = donor_range), alpha=0.50, size=3, width = 0.25) +
  geom_line(data=meandataset, aes(y=val, group=donor_range, color = donor_range), size=1)+
  scale_color_manual(values =c("#1B9E77", "#D95F02", "#7570B3", "#E7298A")) + #comment this line out if you want to use R's auto-color palette
  scale_fill_manual(values=c("No diabetes" = "#1B9E77", "AAb+" = "#D95F02", "T1D INS+" = "#7570B3", "T1D INS-" = "#E7298A")) +  #comment this line out if you want to use R's auto-color palette
  theme_few() +
  ylab("Endocrine\n Area (%)") +
  xlab("Pancreas Region") +
  labs(color = "Donor Type") +
  # replace none with the following to add the legend back into the figure: c(.785,.90)    
  theme(legend.position = "none",legend.text=element_text(size=18, face="bold", family="Arial"), legend.title=element_text(size=20, face="bold", family="Arial"),
        axis.text=element_text(size=22, color="black", family="Arial"), axis.title=element_text(size=24, face="bold", family="Arial", color="black"), axis.ticks=element_line(color="black"),
        panel.border = element_rect(color = "black")) +
        scale_y_continuous(limits=c(0,10))+
      geom_signif(y_position=c(8.25, 9.5), xmin=c(2, 1), xmax=c(3, 3),
              annotation=c("***", "***"), tip_length=0, size=1, color="black", textsize=8) #see here https://rdrr.io/cran/ggsignif/man/stat_signif.html


suppfig1_1
save_plot("suppfig1_1.tiff", suppfig1_1, base_aspect_ratio=1.1)

#ggsave("ESM_Fig3.png", dpi = 600)
#save_plot("ESM_Fig3.tiff", ESM_Fig3, dpi=600, base_aspect_ratio=1.5)
  1. 'region'
  2. 'Region_No'
  3. 'INS'
  4. 'Total Tissue Area (mm²)'
  5. 'Islet Area (mm²)'
  6. 'Acinar Area (mm²)'
  7. 'Duct and other Area (mm²)'
  8. 'Islet Area (%) out of total tiss'
  9. 'Acinar Area (%) out of total tis'
  10. 'Duct and Other (%) out of total'
  11. 'Total cells number (acinar +endo'
  12. 'Total islet cell number'
  13. 'islet:cell density(islet cells/i'
  14. 'islets: Avg Cell Area (cell size'
  15. 'Total acinar cell numbers'
  16. 'acinar:cell density(acinar cells'
  17. 'acinar: Avg Cell Area (cell size'
  18. 'acinar: Avg Cytoplasm Area (µm²)'
  19. 'acinar: Avg Nucleus Area (µm²)'
  20. 'nPODCaseID'
  21. 'DonorType'
  22. 'percent_endocrine_area'
  23. 'percent_acinar_area'
  24. 'percent_remaining_area'
  25. 'endocrine_density'
  26. 'acinar_density'
  27. 'endocrine_cell_size'
  28. 'acinar_cell_size'
  29. 'donorgroup'
  30. 'endocrine_cell_size_scale'
  31. 'acinar_cell_size_scale'
  32. 'endocrine_cell_size_scale1'
  33. 'acinar_cell_size_scale1'
  34. 'mean_percent_endocrine_area'
  35. 'mean_percent_acinar_area'
  36. 'mean_percent_remaining_area'
  37. 'mean_endocrine_density'
  38. 'mean_acinar_density'
  39. 'mean_endocrine_cell_size'
  40. 'mean_endocrine_cell_size_scale1'
  41. 'mean_acinar_cell_size_scale1'
  42. 'group_percent_endocrine_area'
  43. 'group_percent_acinar_area'
  44. 'group_percent_remaining_area'
  45. 'group_endocrine_density'
  46. 'group_acinar_density'
  47. 'group_endocrine_cell_size'
  48. 'group_endocrine_cell_size_scale1'
  49. 'group_acinar_cell_size_scale1'
  50. 'pancreas_region'
  51. 'donor_range'
A data.frame: 12 × 3
donor_rangepancreas_regionval
<fct><fct><dbl>
No diabetesHead2.0008790
No diabetesBody1.9673209
No diabetesTail2.9109851
AAb+ Head1.2927763
AAb+ Body1.5376332
AAb+ Tail2.4773123
T1D INS+ Head0.6938312
T1D INS+ Body0.7619175
T1D INS+ Tail1.2712940
T1D INS- Head0.4580116
T1D INS- Body0.8301359
T1D INS- Tail1.3447566
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In [112]:
dataset <- import("cell3.csv")

dataset %<>% mutate(pancreas_region = ifelse(region == "PH", "Head",
                                             ifelse(region == "PB", "Body",
                                                    "Tail")),
                    donor_range = ifelse(donorgroup == "No diabetes", "No diabetes",
                                       ifelse(donorgroup == "Autoab Pos", "AAb+",
                                              ifelse(donorgroup == "Ins. pos. T1D", "T1D INS+",
                                                    "T1D INS-"))))
dataset$nPODCaseID <- as.character(dataset$nPODCaseID)


#order the variables
dataset <- within(dataset,pancreas_region <- factor(pancreas_region,
                                            levels=rev(c("Tail",
                                                     "Body",
                                                     "Head"))))

dataset <- within(dataset,donor_range <- factor(donor_range,
                                            levels=rev(c("T1D INS-",
                                                     "T1D INS+",
                                                     "AAb+",
                                                        "No diabetes"))))

colnames(dataset)

#need to calculate means at each level of each group, to plot simple effects 
meandataset <- ddply(dataset,.(donor_range,pancreas_region),summarise, val = mean(percent_acinar_area))
meandataset

p <- ggplot(dataset, aes(pancreas_region, percent_acinar_area))


suppfig1_2<-p + geom_jitter(aes(color = donor_range), alpha=0.50, size=3, width = 0.25) +
  geom_line(data=meandataset, aes(y=val, group=donor_range, color = donor_range), size=1)+
  scale_color_manual(values =c("#1B9E77", "#D95F02", "#7570B3", "#E7298A")) + #comment this line out if you want to use R's auto-color palette
  scale_fill_manual(values=c("No diabetes" = "#1B9E77", "AAb+" = "#D95F02", "T1D INS+" = "#7570B3", "T1D INS-" = "#E7298A")) +  #comment this line out if you want to use R's auto-color palette
  theme_few() +
  ylab("Acinar\n Area (%)") +
  xlab("Pancreas Region") +
  labs(color = "Donor Type") +
  # replace none with the following to add the legend back into the figure: c(.785,.90)    
  theme(legend.position = "none",legend.text=element_text(size=18, face="bold", family="Arial"), legend.title=element_text(size=20, face="bold", family="Arial"),
        axis.text=element_text(size=22, color="black", family="Arial"), axis.title=element_text(size=24, face="bold", family="Arial", color="black"), axis.ticks=element_line(color="black"),
        panel.border = element_rect(color = "black")) +
        scale_y_continuous(limits=c(50,100))

suppfig1_2
save_plot("suppfig1_2.tiff", suppfig1_2, base_aspect_ratio=1.1)

#ggsave("ESM_Fig3.png", dpi = 600)
#save_plot("ESM_Fig3.tiff", ESM_Fig3, dpi=600, base_aspect_ratio=1.5)
  1. 'region'
  2. 'Region_No'
  3. 'INS'
  4. 'Total Tissue Area (mm²)'
  5. 'Islet Area (mm²)'
  6. 'Acinar Area (mm²)'
  7. 'Duct and other Area (mm²)'
  8. 'Islet Area (%) out of total tiss'
  9. 'Acinar Area (%) out of total tis'
  10. 'Duct and Other (%) out of total'
  11. 'Total cells number (acinar +endo'
  12. 'Total islet cell number'
  13. 'islet:cell density(islet cells/i'
  14. 'islets: Avg Cell Area (cell size'
  15. 'Total acinar cell numbers'
  16. 'acinar:cell density(acinar cells'
  17. 'acinar: Avg Cell Area (cell size'
  18. 'acinar: Avg Cytoplasm Area (µm²)'
  19. 'acinar: Avg Nucleus Area (µm²)'
  20. 'nPODCaseID'
  21. 'DonorType'
  22. 'percent_endocrine_area'
  23. 'percent_acinar_area'
  24. 'percent_remaining_area'
  25. 'endocrine_density'
  26. 'acinar_density'
  27. 'endocrine_cell_size'
  28. 'acinar_cell_size'
  29. 'donorgroup'
  30. 'endocrine_cell_size_scale'
  31. 'acinar_cell_size_scale'
  32. 'endocrine_cell_size_scale1'
  33. 'acinar_cell_size_scale1'
  34. 'mean_percent_endocrine_area'
  35. 'mean_percent_acinar_area'
  36. 'mean_percent_remaining_area'
  37. 'mean_endocrine_density'
  38. 'mean_acinar_density'
  39. 'mean_endocrine_cell_size'
  40. 'mean_endocrine_cell_size_scale1'
  41. 'mean_acinar_cell_size_scale1'
  42. 'group_percent_endocrine_area'
  43. 'group_percent_acinar_area'
  44. 'group_percent_remaining_area'
  45. 'group_endocrine_density'
  46. 'group_acinar_density'
  47. 'group_endocrine_cell_size'
  48. 'group_endocrine_cell_size_scale1'
  49. 'group_acinar_cell_size_scale1'
  50. 'pancreas_region'
  51. 'donor_range'
A data.frame: 12 × 3
donor_rangepancreas_regionval
<fct><fct><dbl>
No diabetesHead73.38269
No diabetesBody75.91032
No diabetesTail76.68290
AAb+ Head70.36372
AAb+ Body76.64800
AAb+ Tail78.53774
T1D INS+ Head71.76182
T1D INS+ Body72.80789
T1D INS+ Tail77.34036
T1D INS- Head72.62985
T1D INS- Body70.82866
T1D INS- Tail64.55483
Warning message:
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In [113]:
dataset <- import("cell3.csv")

dataset %<>% mutate(pancreas_region = ifelse(region == "PH", "Head",
                                             ifelse(region == "PB", "Body",
                                                    "Tail")),
                    donor_range = ifelse(donorgroup == "No diabetes", "No diabetes",
                                       ifelse(donorgroup == "Autoab Pos", "AAb+",
                                              ifelse(donorgroup == "Ins. pos. T1D", "T1D INS+",
                                                    "T1D INS-"))))
dataset$nPODCaseID <- as.character(dataset$nPODCaseID)


#order the variables
dataset <- within(dataset,pancreas_region <- factor(pancreas_region,
                                            levels=rev(c("Tail",
                                                     "Body",
                                                     "Head"))))

dataset <- within(dataset,donor_range <- factor(donor_range,
                                            levels=rev(c("T1D INS-",
                                                     "T1D INS+",
                                                     "AAb+",
                                                        "No diabetes"))))

colnames(dataset)

#need to calculate means at each level of each group, to plot simple effects 
meandataset <- ddply(dataset,.(donor_range,pancreas_region),summarise, val = mean(percent_remaining_area))
meandataset

p <- ggplot(dataset, aes(pancreas_region, percent_remaining_area))


suppfig1_3<-p + geom_jitter(aes(color = donor_range), alpha=0.50, size=3, width = 0.25) +
  geom_line(data=meandataset, aes(y=val, group=donor_range, color = donor_range), size=1)+
  scale_color_manual(values =c("#1B9E77", "#D95F02", "#7570B3", "#E7298A")) + #comment this line out if you want to use R's auto-color palette
  scale_fill_manual(values=c("No diabetes" = "#1B9E77", "AAb+" = "#D95F02", "T1D INS+" = "#7570B3", "T1D INS-" = "#E7298A")) +  #comment this line out if you want to use R's auto-color palette
  theme_few() +
  ylab("Ductal/Other\n Area (%)") +
  xlab("Pancreas Region") +
  labs(color = "Donor Type") +
  # replace none with the following to add the legend back into the figure: c(.785,.90)    
  theme(legend.position = "none",legend.text=element_text(size=18, face="bold", family="Arial"), legend.title=element_text(size=20, face="bold", family="Arial"),
        axis.text=element_text(size=22, color="black", family="Arial"), axis.title=element_text(size=24, face="bold", family="Arial", color="black"), axis.ticks=element_line(color="black"),
        panel.border = element_rect(color = "black"))+
        scale_y_continuous(limits=c(0,50)) +
      geom_signif(y_position=c(47.5), xmin=c(1), xmax=c(3),
              annotation=c("**"), tip_length=0, size=1, color="black", textsize=8) #see here https://rdrr.io/cran/ggsignif/man/stat_signif.html

suppfig1_3
save_plot("suppfig1_3.tiff", suppfig1_3, base_aspect_ratio=1.1)
#ggsave("ESM_Fig3.png", dpi = 600)
#save_plot("ESM_Fig3.tiff", ESM_Fig3, dpi=600, base_aspect_ratio=1.5)
  1. 'region'
  2. 'Region_No'
  3. 'INS'
  4. 'Total Tissue Area (mm²)'
  5. 'Islet Area (mm²)'
  6. 'Acinar Area (mm²)'
  7. 'Duct and other Area (mm²)'
  8. 'Islet Area (%) out of total tiss'
  9. 'Acinar Area (%) out of total tis'
  10. 'Duct and Other (%) out of total'
  11. 'Total cells number (acinar +endo'
  12. 'Total islet cell number'
  13. 'islet:cell density(islet cells/i'
  14. 'islets: Avg Cell Area (cell size'
  15. 'Total acinar cell numbers'
  16. 'acinar:cell density(acinar cells'
  17. 'acinar: Avg Cell Area (cell size'
  18. 'acinar: Avg Cytoplasm Area (µm²)'
  19. 'acinar: Avg Nucleus Area (µm²)'
  20. 'nPODCaseID'
  21. 'DonorType'
  22. 'percent_endocrine_area'
  23. 'percent_acinar_area'
  24. 'percent_remaining_area'
  25. 'endocrine_density'
  26. 'acinar_density'
  27. 'endocrine_cell_size'
  28. 'acinar_cell_size'
  29. 'donorgroup'
  30. 'endocrine_cell_size_scale'
  31. 'acinar_cell_size_scale'
  32. 'endocrine_cell_size_scale1'
  33. 'acinar_cell_size_scale1'
  34. 'mean_percent_endocrine_area'
  35. 'mean_percent_acinar_area'
  36. 'mean_percent_remaining_area'
  37. 'mean_endocrine_density'
  38. 'mean_acinar_density'
  39. 'mean_endocrine_cell_size'
  40. 'mean_endocrine_cell_size_scale1'
  41. 'mean_acinar_cell_size_scale1'
  42. 'group_percent_endocrine_area'
  43. 'group_percent_acinar_area'
  44. 'group_percent_remaining_area'
  45. 'group_endocrine_density'
  46. 'group_acinar_density'
  47. 'group_endocrine_cell_size'
  48. 'group_endocrine_cell_size_scale1'
  49. 'group_acinar_cell_size_scale1'
  50. 'pancreas_region'
  51. 'donor_range'
A data.frame: 12 × 3
donor_rangepancreas_regionval
<fct><fct><dbl>
No diabetesHead24.61643
No diabetesBody22.12236
No diabetesTail20.40611
AAb+ Head28.34350
AAb+ Body21.81436
AAb+ Tail18.98495
T1D INS+ Head27.54435
T1D INS+ Body26.43019
T1D INS+ Tail21.38835
T1D INS- Head26.91214
T1D INS- Body28.34120
T1D INS- Tail34.10041
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In [114]:
suppfig1<-plot_grid(suppfig1_1, suppfig1_2,  suppfig1_3, nrow=1, ncol=3, 
                #labels="B", 
                #label_size=30,
               label_x=0,
               label_y=1)





#features like expand=() expand_limits()  expand=expand_scale()

save_plot("suppfig1.tiff", suppfig1, ncol=3, nrow=1, base_aspect_ratio=1.1)
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statistical analysis for supplemental figure 1 and figure 3a

In [115]:
/*this macro is used for other figures besides supp figure 1.
this macro is used to analyze critical cell and duct endpoints using mixed model.  
First step is to explore the best covariance structure for each endpoint, then identify if differences exist.  */

/*
Covariance structures considered include:
homogeneous covariance structures
vc - simpJlist, correlation of errors assumed to be 0
cs - compound symmetry, constant variance and covariance

heterogeneous covariance structure
un - unstructured, most complex
unr- unstructured correlation
un(1) - banded main diagonal
csh - heterogeneous compound symmetry
hf - Huynh-Feldt (similar to csh) 
arh(1) - autoregressive heterogeneous
*/


%macro explore (a);

PROC mixed data=cell3 /*maxiter=1000 maxfunc=5000  can also use covtest*/;
     class nPODCaseID donorgroup region;
     model  &a= region|donorgroup/solution; /*can use  ddfm = kenwardroger after solution for unbalanced data to improve performance of t and f tests*/
     /*option e3 after solution helps to describe how type 3 tests were constructed*/
     repeated  region/ subject=nPODCaseID(donorgroup)  type=vc; 
     ods output FitStatistics=Fitvc(rename=(value=vc)) Dimensions=Parmvc(rename=(value=Numvc)) ConvergenceStatus=ConvergeStatusvc; 
     /*lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;*/
run;
DATA ConvergeStatusvc;
    set ConvergeStatusvc;
    covar="vc ";
RUN;

PROC mixed data=cell3 /*maxiter=1000 maxfunc=5000  can also use covtest*/;
     class nPODCaseID donorgroup region;
     model  &a= region|donorgroup/solution; /*can use  ddfm = kenwardroger after solution for unbalanced data to improve performance of t and f tests*/
     /*option e3 after solution helps to describe how type 3 tests were constructed*/
     repeated  region/ subject=nPODCaseID(donorgroup)   type=cs; 
     ods output FitStatistics=Fitcs(rename=(value=cs)) Dimensions=Parmcs(rename=(value=Numcs)) ConvergenceStatus=ConvergeStatuscs;  
     /*lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;*/
run;
DATA ConvergeStatuscs;
    set ConvergeStatuscs;
    covar="cs ";
RUN;

PROC mixed data=cell3 /*maxiter=1000 maxfunc=5000  can also use covtest*/;
     class nPODCaseID donorgroup region;
     model  &a= region|donorgroup/solution;/*can use  ddfm = kenwardroger after solution for unbalanced data to improve performance of t and f tests*/
     /*option e3 after solution helps to describe how type 3 tests were constructed*/
     repeated  region/ subject=nPODCaseID(donorgroup)   type=un; 
     ods output FitStatistics=Fitun(rename=(value=un)) Dimensions=Parmun(rename=(value=Numun)) ConvergenceStatus=ConvergeStatusun;  
     /*lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;*/
run;
DATA ConvergeStatusun;
    set ConvergeStatusun;
    covar="un ";
RUN;

PROC mixed data=cell3 /*maxiter=1000 maxfunc=5000  can also use covtest*/;
     class nPODCaseID donorgroup region;
     model  &a= region|donorgroup/solution; /*can use  ddfm = kenwardroger after solution for unbalanced data to improve performance of t and f tests*/
     /*option e3 after solution helps to describe how type 3 tests were constructed*/
     repeated  region/ subject=nPODCaseID(donorgroup)   type=unr; 
     ods output FitStatistics=Fitunr(rename=(value=unr)) Dimensions=Parmunr(rename=(value=Numunr)) ConvergenceStatus=ConvergeStatusunr;  
     /*lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;*/
run;
DATA ConvergeStatusunr;
    set ConvergeStatusunr;
    covar="unr";
RUN;

PROC mixed data=cell3 /*maxiter=1000 maxfunc=5000  can also use covtest*/;
     class nPODCaseID donorgroup region;
     model  &a= region|donorgroup/solution; /*can use  ddfm = kenwardroger after solution for unbalanced data to improve performance of t and f tests*/
     /*option e3 after solution helps to describe how type 3 tests were constructed*/
     repeated  region/ subject=nPODCaseID(donorgroup)  type=un(1); 
     ods output FitStatistics=Fitun1(rename=(value=un1)) Dimensions=Parmun1(rename=(value=Numun1)) ConvergenceStatus=ConvergeStatusun1;  
     parms/ols;
     /*lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;*/
run;
DATA ConvergeStatusun1;
    set ConvergeStatusun1;
    covar="un1";
RUN;

PROC mixed data=cell3 /*maxiter=1000 maxfunc=5000  can also use covtest*/;
     class nPODCaseID donorgroup region;
     model  &a= region|donorgroup/solution; /*can use  ddfm = kenwardroger after solution for unbalanced data to improve performance of t and f tests*/
     /*option e3 after solution helps to describe how type 3 tests were constructed*/
     repeated  region/ subject=nPODCaseID(donorgroup)  type=csh; 
     ods output FitStatistics=Fitcsh(rename=(value=csh)) Dimensions=Parmcsh(rename=(value=Numcsh)) ConvergenceStatus=ConvergeStatuscsh; 
     /*lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;*/
run;
DATA ConvergeStatuscsh;
    set ConvergeStatuscsh;
    covar="csh";
RUN;

PROC mixed data=cell3 /*maxiter=1000 maxfunc=5000  can also use covtest*/;
     class nPODCaseID donorgroup region;
     model  &a= region|donorgroup/solution; /*can use  ddfm = kenwardroger after solution for unbalanced data to improve performance of t and f tests*/
     /*option e3 after solution helps to describe how type 3 tests were constructed*/
     repeated  region/ subject=nPODCaseID(donorgroup)  type=hf; 
     ods output FitStatistics=Fithf(rename=(value=hf)) Dimensions=Parmhf(rename=(value=Numhf)) ConvergenceStatus=ConvergeStatushf;
     /*lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;*/
run;
DATA ConvergeStatushf;
    set ConvergeStatushf;
    covar="hf ";
RUN;

PROC mixed data=cell3 /*maxiter=1000 maxfunc=5000  can also use covtest*/;
     class nPODCaseID donorgroup region;
     model  &a= region|donorgroup/solution; /*can use  ddfm = kenwardroger after solution for unbalanced data to improve performance of t and f tests*/
     /*option e3 after solution helps to describe how type 3 tests were constructed*/
     repeated  region/ subject=nPODCaseID(donorgroup)  type=arh(1); 
     ods output FitStatistics=Fitarh1(rename=(value=arh1)) Dimensions=Parmarh1(rename=(value=Numarh1)) ConvergenceStatus=ConvergeStatusarh1;
     /*lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;*/
run;
DATA ConvergeStatusarh1;
    set ConvergeStatusarh1;
    covar="arh(1) ";
RUN;

DATA all;
    merge work.fit:;
RUN;

/*above merge line merges all files with the prefix fit.  The reason for this instead of spelling out each file is because 
some fitstatistics files do not exist for each covar structure tested*/

PROC print data=all label noobs;
RUN;

DATA STATUS;
    set ConvergeStatus:;
RUN;

proc print data=status; run;

%mend explore;
Out[115]:

75                                                         The SAS System                         22:22 Wednesday, November 11, 2020

13515 ods listing close;ods html5 (id=saspy_internal) file=_tomods1 options(bitmap_mode='inline') device=svg style=HTMLBlue;
13515 ! ods graphics on / outputfmt=png;
NOTE: Writing HTML5(SASPY_INTERNAL) Body file: _TOMODS1
13516
13517 /*this macro is used for other figures besides supp figure 1.
13518 this macro is used to analyze critical cell and duct endpoints using mixed model.
13519 First step is to explore the best covariance structure for each endpoint, then identify if differences exist. */
13520
13521 /*
13522 Covariance structures considered include:
13523 homogeneous covariance structures
13524 vc - simpJlist, correlation of errors assumed to be 0
13525 cs - compound symmetry, constant variance and covariance
13526
13527 heterogeneous covariance structure
13528 un - unstructured, most complex
13529 unr- unstructured correlation
13530 un(1) - banded main diagonal
13531 csh - heterogeneous compound symmetry
13532 hf - Huynh-Feldt (similar to csh)
13533 arh(1) - autoregressive heterogeneous
13534 */
13535
13536
13537 %macro explore (a);
13538
13539 PROC mixed data=cell3 /*maxiter=1000 maxfunc=5000 can also use covtest*/;
13540 class nPODCaseID donorgroup region;
13541 model &a= region|donorgroup/solution; /*can use ddfm = kenwardroger after solution for unbalanced data to improve
13541 ! performance of t and f tests*/
13542 /*option e3 after solution helps to describe how type 3 tests were constructed*/
13543 repeated region/ subject=nPODCaseID(donorgroup) type=vc;
13544 ods output FitStatistics=Fitvc(rename=(value=vc)) Dimensions=Parmvc(rename=(value=Numvc))
13544 ! ConvergenceStatus=ConvergeStatusvc;
13545 /*lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;*/
13546 run;
13547 DATA ConvergeStatusvc;
13548 set ConvergeStatusvc;
13549 covar="vc ";
13550 RUN;
13551
13552 PROC mixed data=cell3 /*maxiter=1000 maxfunc=5000 can also use covtest*/;
13553 class nPODCaseID donorgroup region;
13554 model &a= region|donorgroup/solution; /*can use ddfm = kenwardroger after solution for unbalanced data to improve
13554 ! performance of t and f tests*/
13555 /*option e3 after solution helps to describe how type 3 tests were constructed*/
13556 repeated region/ subject=nPODCaseID(donorgroup) type=cs;
13557 ods output FitStatistics=Fitcs(rename=(value=cs)) Dimensions=Parmcs(rename=(value=Numcs))
13557 ! ConvergenceStatus=ConvergeStatuscs;
13558 /*lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;*/
13559 run;
13560 DATA ConvergeStatuscs;
13561 set ConvergeStatuscs;
13562 covar="cs ";
13563 RUN;
13564
13565 PROC mixed data=cell3 /*maxiter=1000 maxfunc=5000 can also use covtest*/;
13566 class nPODCaseID donorgroup region;
13567 model &a= region|donorgroup/solution;/*can use ddfm = kenwardroger after solution for unbalanced data to improve
13567 ! performance of t and f tests*/
13568 /*option e3 after solution helps to describe how type 3 tests were constructed*/
13569 repeated region/ subject=nPODCaseID(donorgroup) type=un;
13570 ods output FitStatistics=Fitun(rename=(value=un)) Dimensions=Parmun(rename=(value=Numun))
13570 ! ConvergenceStatus=ConvergeStatusun;
13571 /*lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;*/
13572 run;
13573 DATA ConvergeStatusun;
13574 set ConvergeStatusun;
13575 covar="un ";
13576 RUN;
13577
13578 PROC mixed data=cell3 /*maxiter=1000 maxfunc=5000 can also use covtest*/;
13579 class nPODCaseID donorgroup region;
13580 model &a= region|donorgroup/solution; /*can use ddfm = kenwardroger after solution for unbalanced data to improve
13580 ! performance of t and f tests*/
13581 /*option e3 after solution helps to describe how type 3 tests were constructed*/
13582 repeated region/ subject=nPODCaseID(donorgroup) type=unr;
13583 ods output FitStatistics=Fitunr(rename=(value=unr)) Dimensions=Parmunr(rename=(value=Numunr))
13583 ! ConvergenceStatus=ConvergeStatusunr;
13584 /*lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;*/
13585 run;
13586 DATA ConvergeStatusunr;
13587 set ConvergeStatusunr;
13588 covar="unr";
13589 RUN;
13590
13591 PROC mixed data=cell3 /*maxiter=1000 maxfunc=5000 can also use covtest*/;
13592 class nPODCaseID donorgroup region;
13593 model &a= region|donorgroup/solution; /*can use ddfm = kenwardroger after solution for unbalanced data to improve
13593 ! performance of t and f tests*/
13594 /*option e3 after solution helps to describe how type 3 tests were constructed*/
13595 repeated region/ subject=nPODCaseID(donorgroup) type=un(1);
13596 ods output FitStatistics=Fitun1(rename=(value=un1)) Dimensions=Parmun1(rename=(value=Numun1))
13596 ! ConvergenceStatus=ConvergeStatusun1;
13597 parms/ols;
13598 /*lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;*/
13599 run;
13600 DATA ConvergeStatusun1;
13601 set ConvergeStatusun1;
13602 covar="un1";
13603 RUN;
13604
13605 PROC mixed data=cell3 /*maxiter=1000 maxfunc=5000 can also use covtest*/;
13606 class nPODCaseID donorgroup region;
13607 model &a= region|donorgroup/solution; /*can use ddfm = kenwardroger after solution for unbalanced data to improve
13607 ! performance of t and f tests*/
13608 /*option e3 after solution helps to describe how type 3 tests were constructed*/
13609 repeated region/ subject=nPODCaseID(donorgroup) type=csh;
13610 ods output FitStatistics=Fitcsh(rename=(value=csh)) Dimensions=Parmcsh(rename=(value=Numcsh))
13610 ! ConvergenceStatus=ConvergeStatuscsh;
13611 /*lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;*/
13612 run;
13613 DATA ConvergeStatuscsh;
13614 set ConvergeStatuscsh;
13615 covar="csh";
13616 RUN;
13617
13618 PROC mixed data=cell3 /*maxiter=1000 maxfunc=5000 can also use covtest*/;
13619 class nPODCaseID donorgroup region;
13620 model &a= region|donorgroup/solution; /*can use ddfm = kenwardroger after solution for unbalanced data to improve
13620 ! performance of t and f tests*/
13621 /*option e3 after solution helps to describe how type 3 tests were constructed*/
13622 repeated region/ subject=nPODCaseID(donorgroup) type=hf;
13623 ods output FitStatistics=Fithf(rename=(value=hf)) Dimensions=Parmhf(rename=(value=Numhf))
13623 ! ConvergenceStatus=ConvergeStatushf;
13624 /*lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;*/
13625 run;
13626 DATA ConvergeStatushf;
13627 set ConvergeStatushf;
13628 covar="hf ";
13629 RUN;
13630
13631 PROC mixed data=cell3 /*maxiter=1000 maxfunc=5000 can also use covtest*/;
13632 class nPODCaseID donorgroup region;
13633 model &a= region|donorgroup/solution; /*can use ddfm = kenwardroger after solution for unbalanced data to improve
13633 ! performance of t and f tests*/
13634 /*option e3 after solution helps to describe how type 3 tests were constructed*/
13635 repeated region/ subject=nPODCaseID(donorgroup) type=arh(1);
13636 ods output FitStatistics=Fitarh1(rename=(value=arh1)) Dimensions=Parmarh1(rename=(value=Numarh1))
13636 ! ConvergenceStatus=ConvergeStatusarh1;
13637 /*lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;*/
13638 run;
13639 DATA ConvergeStatusarh1;
13640 set ConvergeStatusarh1;
13641 covar="arh(1) ";
13642 RUN;
13643
13644 DATA all;
13645 merge work.fit:;
13646 RUN;
13647
13648 /*above merge line merges all files with the prefix fit. The reason for this instead of spelling out each file is
13648 ! because
13649 some fitstatistics files do not exist for each covar structure tested*/
13650
13651 PROC print data=all label noobs;
13652 RUN;
13653
13654 DATA STATUS;
13655 set ConvergeStatus:;
13656 RUN;
13657
13658 proc print data=status; run;
13659
13660 %mend explore;
13661
13662
13663
13664 ods html5 (id=saspy_internal) close;ods listing;
13665
In [116]:
%explore(percent_endocrine_area);
Out[116]:
SAS Output

SAS Output

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable percent_endocrine_area
Covariance Structure Variance Components
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method Parameter
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 1
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 210.12944737  
1 1 210.12944737 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
region nPODCaseI(donorgrou) 0.3475

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 210.1
AIC (Smaller is Better) 212.1
AICC (Smaller is Better) 212.2
BIC (Smaller is Better) 213.8

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
0 0.00 1.0000

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     2.9110 0.1576 35 18.48 <.0001
region   PB -0.9437 0.2271 68 -4.16 <.0001
region   PH -0.9101 0.2228 68 -4.08 0.0001
region   PT 0 . . . .
donorgroup Autoab Pos   -0.4337 0.2613 35 -1.66 0.1059
donorgroup Ins. neg. T1D   -1.5662 0.2729 35 -5.74 <.0001
donorgroup Ins. pos. T1D   -1.6397 0.2441 35 -6.72 <.0001
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB 0.003985 0.3721 68 0.01 0.9915
donorgroup*region Autoab Pos PH -0.2744 0.3778 68 -0.73 0.4701
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB 0.4290 0.3884 68 1.10 0.2732
donorgroup*region Ins. neg. T1D PH 0.02336 0.3859 68 0.06 0.9519
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 0.4343 0.3479 68 1.25 0.2162
donorgroup*region Ins. pos. T1D PH 0.3326 0.3452 68 0.96 0.3386
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 23.24 <.0001
donorgroup 3 35 43.64 <.0001
donorgroup*region 6 68 0.68 0.6643

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable percent_endocrine_area
Covariance Structure Compound Symmetry
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method Profile
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 2
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 210.12944737  
1 2 180.02751019 0.02850241
2 1 179.88264364 0.00074851
3 1 179.87905269 0.00000062
4 1 179.87904978 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
CS nPODCaseI(donorgrou) 0.2193
Residual   0.1460

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 179.9
AIC (Smaller is Better) 183.9
AICC (Smaller is Better) 184.0
BIC (Smaller is Better) 187.2

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
1 30.25 <.0001

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     2.9110 0.1615 35 18.02 <.0001
region   PB -0.8507 0.1482 68 -5.74 <.0001
region   PH -0.9101 0.1444 68 -6.30 <.0001
region   PT 0 . . . .
donorgroup Autoab Pos   -0.4337 0.2679 35 -1.62 0.1144
donorgroup Ins. neg. T1D   -1.5662 0.2798 35 -5.60 <.0001
donorgroup Ins. pos. T1D   -1.6397 0.2503 35 -6.55 <.0001
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB -0.08897 0.2418 68 -0.37 0.7140
donorgroup*region Autoab Pos PH -0.1717 0.2469 68 -0.70 0.4890
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB 0.3361 0.2523 68 1.33 0.1873
donorgroup*region Ins. neg. T1D PH 0.02336 0.2501 68 0.09 0.9259
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 0.3413 0.2262 68 1.51 0.1359
donorgroup*region Ins. pos. T1D PH 0.3326 0.2237 68 1.49 0.1417
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 51.84 <.0001
donorgroup 3 35 19.96 <.0001
donorgroup*region 6 68 1.17 0.3338

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable percent_endocrine_area
Covariance Structure Unstructured
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 6
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 210.12944737  
1 4 169.75403581 0.05516690
2 1 169.14235830 0.00336520
3 1 169.10667775 0.00002485
4 1 169.10642540 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
UN(1,1) nPODCaseI(donorgrou) 0.2877
UN(2,1) nPODCaseI(donorgrou) 0.1702
UN(2,2) nPODCaseI(donorgrou) 0.2520
UN(3,1) nPODCaseI(donorgrou) 0.2621
UN(3,2) nPODCaseI(donorgrou) 0.2055
UN(3,3) nPODCaseI(donorgrou) 0.5388

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 169.1
AIC (Smaller is Better) 181.1
AICC (Smaller is Better) 182.0
BIC (Smaller is Better) 191.1

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
5 41.02 <.0001

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     2.9110 0.1962 35 14.84 <.0001
region   PB -0.8578 0.1494 35 -5.74 <.0001
region   PH -0.9101 0.1647 35 -5.53 <.0001
region   PT 0 . . . .
donorgroup Autoab Pos   -0.4337 0.3253 35 -1.33 0.1911
donorgroup Ins. neg. T1D   -1.5662 0.3398 35 -4.61 <.0001
donorgroup Ins. pos. T1D   -1.6397 0.3039 35 -5.40 <.0001
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB -0.08186 0.2452 35 -0.33 0.7405
donorgroup*region Autoab Pos PH -0.1968 0.2778 35 -0.71 0.4834
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB 0.3432 0.2559 35 1.34 0.1886
donorgroup*region Ins. neg. T1D PH 0.02336 0.2853 35 0.08 0.9352
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 0.3484 0.2292 35 1.52 0.1375
donorgroup*region Ins. pos. T1D PH 0.3326 0.2552 35 1.30 0.2009
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 35 38.84 <.0001
donorgroup 3 35 20.37 <.0001
donorgroup*region 6 35 1.18 0.3410

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable percent_endocrine_area
Covariance Structure Unstructured using Correlations
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 6
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 210.12944737  
1 2 170.67583961 0.12606959
2 1 169.29757068 0.01622832
3 1 169.11484928 0.00080443
4 1 169.10644935 0.00000237
5 1 169.10642538 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 0.2877
Var(2) nPODCaseI(donorgrou) 0.2520
Var(3) nPODCaseI(donorgrou) 0.5388
Corr(2,1) nPODCaseI(donorgrou) 0.6322
Corr(3,1) nPODCaseI(donorgrou) 0.6657
Corr(3,2) nPODCaseI(donorgrou) 0.5577

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 169.1
AIC (Smaller is Better) 181.1
AICC (Smaller is Better) 182.0
BIC (Smaller is Better) 191.1

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
5 41.02 <.0001

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     2.9110 0.1962 35 14.84 <.0001
region   PB -0.8578 0.1494 35 -5.74 <.0001
region   PH -0.9101 0.1647 35 -5.53 <.0001
region   PT 0 . . . .
donorgroup Autoab Pos   -0.4337 0.3253 35 -1.33 0.1911
donorgroup Ins. neg. T1D   -1.5662 0.3398 35 -4.61 <.0001
donorgroup Ins. pos. T1D   -1.6397 0.3039 35 -5.40 <.0001
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB -0.08185 0.2452 35 -0.33 0.7405
donorgroup*region Autoab Pos PH -0.1968 0.2778 35 -0.71 0.4834
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB 0.3432 0.2559 35 1.34 0.1886
donorgroup*region Ins. neg. T1D PH 0.02336 0.2853 35 0.08 0.9352
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 0.3484 0.2292 35 1.52 0.1375
donorgroup*region Ins. pos. T1D PH 0.3326 0.2552 35 1.30 0.2009
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 35 38.84 <.0001
donorgroup 3 35 20.37 <.0001
donorgroup*region 6 35 1.18 0.3410

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable percent_endocrine_area
Covariance Structure Banded
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 6
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 2 203.29531611  
1 39 221.97068939 78.62853350
2 39 221.97068939 78.62853350
3 39 221.97068939 78.62853350

Convergence Status

WARNING: Stopped because of too many likelihood evaluations.

Covariance Parameter Values At Last Iteration

Covariance Parameter Values At Last Iteration
Cov Parm Subject Estimate
UN(1,1) nPODCaseI(donorgrou) 0.5453
UN(2,1) nPODCaseI(donorgrou) 0
UN(2,2) nPODCaseI(donorgrou) 0.5000
UN(3,1) nPODCaseI(donorgrou) 0
UN(3,2) nPODCaseI(donorgrou) 0
UN(3,3) nPODCaseI(donorgrou) 0.9288

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable percent_endocrine_area
Covariance Structure Heterogeneous Compound Symmetry
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 4
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 210.12944737  
1 2 170.13253549 0.01791882
2 1 169.94742982 0.00032460
3 1 169.94424699 0.00000013
4 1 169.94424570 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 0.2710
Var(2) nPODCaseI(donorgrou) 0.2568
Var(3) nPODCaseI(donorgrou) 0.5438
CSH nPODCaseI(donorgrou) 0.6126

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 169.9
AIC (Smaller is Better) 177.9
AICC (Smaller is Better) 178.4
BIC (Smaller is Better) 184.6

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
3 40.19 <.0001

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     2.9110 0.1971 35 14.77 <.0001
region   PB -0.8713 0.1594 68 -5.47 <.0001
region   PH -0.9101 0.1565 68 -5.82 <.0001
region   PT 0 . . . .
donorgroup Autoab Pos   -0.4337 0.3268 35 -1.33 0.1931
donorgroup Ins. neg. T1D   -1.5662 0.3414 35 -4.59 <.0001
donorgroup Ins. pos. T1D   -1.6397 0.3053 35 -5.37 <.0001
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB -0.06842 0.2617 68 -0.26 0.7945
donorgroup*region Autoab Pos PH -0.1902 0.2642 68 -0.72 0.4739
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB 0.3566 0.2732 68 1.31 0.1961
donorgroup*region Ins. neg. T1D PH 0.02336 0.2710 68 0.09 0.9316
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 0.3619 0.2447 68 1.48 0.1437
donorgroup*region Ins. pos. T1D PH 0.3326 0.2424 68 1.37 0.1745
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 40.61 <.0001
donorgroup 3 35 20.53 <.0001
donorgroup*region 6 68 1.15 0.3435

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable percent_endocrine_area
Covariance Structure Huynh-Feldt
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 4
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 210.12944737  
1 2 174.32598899 0.07631754
2 1 173.69024187 0.00287602
3 1 173.66713174 0.00000623
4 1 173.66708295 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 0.3309
Var(2) nPODCaseI(donorgrou) 0.2672
Var(3) nPODCaseI(donorgrou) 0.4609
HF nPODCaseI(donorgrou) 0.1461

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 173.7
AIC (Smaller is Better) 181.7
AICC (Smaller is Better) 182.1
BIC (Smaller is Better) 188.3

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
3 36.46 <.0001

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     2.9110 0.1814 35 16.04 <.0001
region   PB -0.8454 0.1480 68 -5.71 <.0001
region   PH -0.9101 0.1445 68 -6.30 <.0001
region   PT 0 . . . .
donorgroup Autoab Pos   -0.4337 0.3009 35 -1.44 0.1584
donorgroup Ins. neg. T1D   -1.5662 0.3143 35 -4.98 <.0001
donorgroup Ins. pos. T1D   -1.6397 0.2811 35 -5.83 <.0001
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB -0.09426 0.2417 68 -0.39 0.6978
donorgroup*region Autoab Pos PH -0.1946 0.2454 68 -0.79 0.4305
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB 0.3308 0.2523 68 1.31 0.1941
donorgroup*region Ins. neg. T1D PH 0.02336 0.2502 68 0.09 0.9259
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 0.3360 0.2261 68 1.49 0.1418
donorgroup*region Ins. pos. T1D PH 0.3326 0.2238 68 1.49 0.1418
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 52.40 <.0001
donorgroup 3 35 20.94 <.0001
donorgroup*region 6 68 1.19 0.3218

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable percent_endocrine_area
Covariance Structure Heterogeneous Autoregressive
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 4
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 210.12944737  
1 2 175.42538823 0.02029670
2 1 175.27472468 0.00027748
3 1 175.27275970 0.00000006
4 1 175.27275928 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 0.2493
Var(2) nPODCaseI(donorgrou) 0.2576
Var(3) nPODCaseI(donorgrou) 0.5503
ARH(1) nPODCaseI(donorgrou) 0.5954

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 175.3
AIC (Smaller is Better) 183.3
AICC (Smaller is Better) 183.7
BIC (Smaller is Better) 189.9

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
3 34.86 <.0001

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     2.9110 0.1983 35 14.68 <.0001
region   PB -0.9151 0.1981 68 -4.62 <.0001
region   PH -0.9101 0.1603 68 -5.68 <.0001
region   PT 0 . . . .
donorgroup Autoab Pos   -0.4337 0.3288 35 -1.32 0.1957
donorgroup Ins. neg. T1D   -1.5662 0.3434 35 -4.56 <.0001
donorgroup Ins. pos. T1D   -1.6397 0.3071 35 -5.34 <.0001
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB -0.02460 0.3261 68 -0.08 0.9401
donorgroup*region Autoab Pos PH -0.1750 0.2698 68 -0.65 0.5188
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB 0.4005 0.3405 68 1.18 0.2437
donorgroup*region Ins. neg. T1D PH 0.02336 0.2776 68 0.08 0.9332
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 0.4057 0.3049 68 1.33 0.1877
donorgroup*region Ins. pos. T1D PH 0.3326 0.2483 68 1.34 0.1847
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 38.24 <.0001
donorgroup 3 35 22.63 <.0001
donorgroup*region 6 68 1.11 0.3644

The SAS System

The PRINT Procedure

Data Set WORK.ALL

Description arh1 cs csh hf un unr vc
-2 Res Log Likelihood 175.3 179.9 169.9 173.7 169.1 169.1 210.1
AIC (Smaller is Better) 183.3 183.9 177.9 181.7 181.1 181.1 212.1
AICC (Smaller is Better) 183.7 184.0 178.4 182.1 182.0 182.0 212.2
BIC (Smaller is Better) 189.9 187.2 184.6 188.3 191.1 191.1 213.8

The SAS System

The PRINT Procedure

Data Set WORK.STATUS

Obs Reason Status pdG pdH covar
1 Convergence criteria met. 0 1 1 arh(1)
2 Convergence criteria met. 0 1 1 cs
3 Convergence criteria met. 0 1 1 csh
4 Convergence criteria met. 0 1 1 hf
5 Convergence criteria met. 0 1 1 un
6 WARNING: Stopped because of too many likelihood evaluations. 1 1 1 un1
7 Convergence criteria met. 0 1 1 unr
8 Convergence criteria met. 0 1 1 vc
In [117]:
proc sort data=cell3;
by region;
run;

PROC freq data=cell3;
tables donorgroup;
by region;
run;
Out[117]:
SAS Output

SAS Output

The SAS System

The FREQ Procedure

The FREQ Procedure

region=PB

Table donorgroup

One-Way Frequencies

donorgroup Frequency Percent Cumulative
Frequency
Cumulative
Percent
Autoab Pos 8 21.05 8 21.05
Ins. neg. T1D 7 18.42 15 39.47
Ins. pos. T1D 10 26.32 25 65.79
No diabetes 13 34.21 38 100.00

The SAS System

The FREQ Procedure

region=PH

Table donorgroup

One-Way Frequencies

donorgroup Frequency Percent Cumulative
Frequency
Cumulative
Percent
Autoab Pos 7 18.42 7 18.42
Ins. neg. T1D 7 18.42 14 36.84
Ins. pos. T1D 10 26.32 24 63.16
No diabetes 14 36.84 38 100.00

The SAS System

The FREQ Procedure

region=PT

Table donorgroup

One-Way Frequencies

donorgroup Frequency Percent Cumulative
Frequency
Cumulative
Percent
Autoab Pos 8 20.51 8 20.51
Ins. neg. T1D 7 17.95 15 38.46
Ins. pos. T1D 10 25.64 25 64.10
No diabetes 14 35.90 39 100.00
In [118]:
PROC format;
     value $regionformat
     'PH' = '1_H'
     'PB' = '2_B'
     'PT' = '3_T';
     RUN;

PROC mixed data=cell3 /*maxiter=1000 maxfunc=5000  can also use covtest*/;
format region $regionformat.;
class nPODCaseID donorgroup region;
     model  percent_endocrine_area= region|donorgroup/solution; /*can use  ddfm = kenwardroger after solution for unbalanced data to improve performance of t and f tests*/
     /*option e3 after solution helps to describe how type 3 tests were constructed*/
     repeated  region/ subject=nPODCaseID(donorgroup)  type=csh; 
     lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;
     store endocrine_model_data;
run;


/*even though not significant, showing interaction data*/
proc plm restore=endocrine_model_data;
effectplot interaction(sliceby=donorgroup);
slice donorgroup*region/sliceby=donorgroup diff adjust=tukey cl pdiff alpha=0.05 plots=none nof means;
run;
Out[118]:
SAS Output

SAS Output

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable percent_endocrine_area
Covariance Structure Heterogeneous Compound Symmetry
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 1_H 2_B 3_T

Dimensions

Dimensions
Covariance Parameters 4
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 210.12944737  
1 2 170.13253549 0.01791882
2 1 169.94742982 0.00032460
3 1 169.94424699 0.00000013
4 1 169.94424570 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 0.2568
Var(2) nPODCaseI(donorgrou) 0.2710
Var(3) nPODCaseI(donorgrou) 0.5438
CSH nPODCaseI(donorgrou) 0.6126

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 169.9
AIC (Smaller is Better) 177.9
AICC (Smaller is Better) 178.4
BIC (Smaller is Better) 184.6

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
3 40.19 <.0001

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     2.9110 0.1971 35 14.77 <.0001
region   1_H -0.9101 0.1565 68 -5.82 <.0001
region   2_B -0.8713 0.1594 68 -5.47 <.0001
region   3_T 0 . . . .
donorgroup Autoab Pos   -0.4337 0.3268 35 -1.33 0.1931
donorgroup Ins. neg. T1D   -1.5662 0.3414 35 -4.59 <.0001
donorgroup Ins. pos. T1D   -1.6397 0.3053 35 -5.37 <.0001
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos 1_H -0.1902 0.2642 68 -0.72 0.4739
donorgroup*region Autoab Pos 2_B -0.06842 0.2617 68 -0.26 0.7945
donorgroup*region Autoab Pos 3_T 0 . . . .
donorgroup*region Ins. neg. T1D 1_H 0.02336 0.2710 68 0.09 0.9316
donorgroup*region Ins. neg. T1D 2_B 0.3566 0.2732 68 1.31 0.1961
donorgroup*region Ins. neg. T1D 3_T 0 . . . .
donorgroup*region Ins. pos. T1D 1_H 0.3326 0.2424 68 1.37 0.1745
donorgroup*region Ins. pos. T1D 2_B 0.3619 0.2447 68 1.48 0.1437
donorgroup*region Ins. pos. T1D 3_T 0 . . . .
donorgroup*region No diabetes 1_H 0 . . . .
donorgroup*region No diabetes 2_B 0 . . . .
donorgroup*region No diabetes 3_T 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 40.61 <.0001
donorgroup 3 35 20.53 <.0001
donorgroup*region 6 68 1.15 0.3435

Least Squares Means

Least Squares Means
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t| Alpha Lower Upper
region   1_H 1.1324 0.08488 68 13.34 <.0001 0.05 0.9631 1.3018
region   2_B 1.2924 0.08655 68 14.93 <.0001 0.05 1.1196 1.4651
region   3_T 2.0011 0.1222 68 16.38 <.0001 0.05 1.7573 2.2449
donorgroup Autoab Pos   1.7973 0.1804 35 9.96 <.0001 0.05 1.4311 2.1635
donorgroup Ins. neg. T1D   0.8776 0.1920 35 4.57 <.0001 0.05 0.4878 1.2675
donorgroup Ins. pos. T1D   0.9090 0.1607 35 5.66 <.0001 0.05 0.5829 1.2352
donorgroup No diabetes   2.3172 0.1361 35 17.02 <.0001 0.05 2.0409 2.5935
donorgroup*region Autoab Pos 1_H 1.3770 0.1859 68 7.41 <.0001 0.05 1.0060 1.7479
donorgroup*region Autoab Pos 2_B 1.5376 0.1841 68 8.35 <.0001 0.05 1.1703 1.9049
donorgroup*region Autoab Pos 3_T 2.4773 0.2607 68 9.50 <.0001 0.05 1.9570 2.9976
donorgroup*region Ins. neg. T1D 1_H 0.4580 0.1915 68 2.39 0.0196 0.05 0.07580 0.8402
donorgroup*region Ins. neg. T1D 2_B 0.8301 0.1968 68 4.22 <.0001 0.05 0.4375 1.2228
donorgroup*region Ins. neg. T1D 3_T 1.3448 0.2787 68 4.82 <.0001 0.05 0.7886 1.9010
donorgroup*region Ins. pos. T1D 1_H 0.6938 0.1603 68 4.33 <.0001 0.05 0.3740 1.0136
donorgroup*region Ins. pos. T1D 2_B 0.7619 0.1646 68 4.63 <.0001 0.05 0.4334 1.0904
donorgroup*region Ins. pos. T1D 3_T 1.2713 0.2332 68 5.45 <.0001 0.05 0.8059 1.7366
donorgroup*region No diabetes 1_H 2.0009 0.1354 68 14.77 <.0001 0.05 1.7306 2.2711
donorgroup*region No diabetes 2_B 2.0397 0.1420 68 14.37 <.0001 0.05 1.7564 2.3230
donorgroup*region No diabetes 3_T 2.9110 0.1971 68 14.77 <.0001 0.05 2.5177 3.3043

Differences of Least Squares Means

Differences of Least Squares Means
Effect donorgroup region _donorgroup region Estimate Standard
Error
DF t Value Pr > |t| Adjustment Adj P Alpha Lower Upper Adj Lower Adj Upper
region   1_H   2_B -0.1599 0.07630 68 -2.10 0.0398 Tukey-Kramer 0.0982 0.05 -0.3122 -0.00768 -0.3427 0.02288
region   1_H   3_T -0.8687 0.09780 68 -8.88 <.0001 Tukey-Kramer <.0001 0.05 -1.0638 -0.6735 -1.1030 -0.6343
region   2_B   3_T -0.7087 0.09751 68 -7.27 <.0001 Tukey-Kramer <.0001 0.05 -0.9033 -0.5141 -0.9424 -0.4751
donorgroup Autoab Pos   Ins. neg. T1D   0.9197 0.2635 35 3.49 0.0013 Tukey-Kramer 0.0069 0.05 0.3848 1.4545 0.2091 1.6302
donorgroup Autoab Pos   Ins. pos. T1D   0.8883 0.2416 35 3.68 0.0008 Tukey-Kramer 0.0042 0.05 0.3979 1.3787 0.2368 1.5398
donorgroup Autoab Pos   No diabetes   -0.5199 0.2260 35 -2.30 0.0275 Tukey-Kramer 0.1173 0.05 -0.9786 -0.06114 -1.1293 0.08954
donorgroup Ins. neg. T1D   Ins. pos. T1D   -0.03138 0.2504 35 -0.13 0.9010 Tukey-Kramer 0.9993 0.05 -0.5397 0.4769 -0.7066 0.6439
donorgroup Ins. neg. T1D   No diabetes   -1.4396 0.2354 35 -6.12 <.0001 Tukey-Kramer <.0001 0.05 -1.9174 -0.9617 -2.0743 -0.8048
donorgroup Ins. pos. T1D   No diabetes   -1.4082 0.2106 35 -6.69 <.0001 Tukey-Kramer <.0001 0.05 -1.8357 -0.9807 -1.9761 -0.8403
donorgroup*region Autoab Pos 1_H Autoab Pos 2_B -0.1607 0.1674 68 -0.96 0.3406 Tukey-Kramer 0.9981 0.05 -0.4948 0.1734 -0.7273 0.4060
donorgroup*region Autoab Pos 1_H Autoab Pos 3_T -1.1003 0.2128 68 -5.17 <.0001 Tukey-Kramer 0.0001 0.05 -1.5251 -0.6756 -1.8207 -0.3800
donorgroup*region Autoab Pos 1_H Ins. neg. T1D 1_H 0.9190 0.2669 68 3.44 0.0010 Tukey-Kramer 0.0426 0.05 0.3863 1.4516 0.01563 1.8223
donorgroup*region Autoab Pos 1_H Ins. neg. T1D 2_B 0.5468 0.2707 68 2.02 0.0473 Tukey-Kramer 0.6785 0.05 0.006671 1.0870 -0.3693 1.4630
donorgroup*region Autoab Pos 1_H Ins. neg. T1D 3_T 0.03221 0.3350 68 0.10 0.9237 Tukey-Kramer 1.0000 0.05 -0.6363 0.7008 -1.1016 1.1661
donorgroup*region Autoab Pos 1_H Ins. pos. T1D 1_H 0.6831 0.2454 68 2.78 0.0070 Tukey-Kramer 0.2105 0.05 0.1934 1.1729 -0.1475 1.5138
donorgroup*region Autoab Pos 1_H Ins. pos. T1D 2_B 0.6151 0.2483 68 2.48 0.0157 Tukey-Kramer 0.3717 0.05 0.1196 1.1105 -0.2253 1.4554
donorgroup*region Autoab Pos 1_H Ins. pos. T1D 3_T 0.1057 0.2982 68 0.35 0.7242 Tukey-Kramer 1.0000 0.05 -0.4894 0.7008 -0.9036 1.1150
donorgroup*region Autoab Pos 1_H No diabetes 1_H -0.6239 0.2300 68 -2.71 0.0084 Tukey-Kramer 0.2427 0.05 -1.0829 -0.1650 -1.4023 0.1545
donorgroup*region Autoab Pos 1_H No diabetes 2_B -0.6628 0.2339 68 -2.83 0.0061 Tukey-Kramer 0.1897 0.05 -1.1295 -0.1960 -1.4544 0.1289
donorgroup*region Autoab Pos 1_H No diabetes 3_T -1.5340 0.2709 68 -5.66 <.0001 Tukey-Kramer <.0001 0.05 -2.0746 -0.9934 -2.4509 -0.6171
donorgroup*region Autoab Pos 2_B Autoab Pos 3_T -0.9397 0.2075 68 -4.53 <.0001 Tukey-Kramer 0.0014 0.05 -1.3538 -0.5256 -1.6420 -0.2373
donorgroup*region Autoab Pos 2_B Ins. neg. T1D 1_H 1.0796 0.2656 68 4.06 0.0001 Tukey-Kramer 0.0066 0.05 0.5495 1.6097 0.1806 1.9787
donorgroup*region Autoab Pos 2_B Ins. neg. T1D 2_B 0.7075 0.2694 68 2.63 0.0107 Tukey-Kramer 0.2865 0.05 0.1698 1.2452 -0.2044 1.6194
donorgroup*region Autoab Pos 2_B Ins. neg. T1D 3_T 0.1929 0.3340 68 0.58 0.5656 Tukey-Kramer 1.0000 0.05 -0.4737 0.8594 -0.9376 1.3233
donorgroup*region Autoab Pos 2_B Ins. pos. T1D 1_H 0.8438 0.2441 68 3.46 0.0009 Tukey-Kramer 0.0410 0.05 0.3568 1.3308 0.01783 1.6698
donorgroup*region Autoab Pos 2_B Ins. pos. T1D 2_B 0.7757 0.2470 68 3.14 0.0025 Tukey-Kramer 0.0937 0.05 0.2829 1.2685 -0.06007 1.6115
donorgroup*region Autoab Pos 2_B Ins. pos. T1D 3_T 0.2663 0.2971 68 0.90 0.3732 Tukey-Kramer 0.9990 0.05 -0.3265 0.8592 -0.7391 1.2718
donorgroup*region Autoab Pos 2_B No diabetes 1_H -0.4632 0.2285 68 -2.03 0.0466 Tukey-Kramer 0.6738 0.05 -0.9193 -0.00722 -1.2367 0.3102
donorgroup*region Autoab Pos 2_B No diabetes 2_B -0.5021 0.2325 68 -2.16 0.0343 Tukey-Kramer 0.5832 0.05 -0.9660 -0.03823 -1.2888 0.2846
donorgroup*region Autoab Pos 2_B No diabetes 3_T -1.3734 0.2697 68 -5.09 <.0001 Tukey-Kramer 0.0002 0.05 -1.9115 -0.8352 -2.2860 -0.4607
donorgroup*region Autoab Pos 3_T Ins. neg. T1D 1_H 2.0193 0.3235 68 6.24 <.0001 Tukey-Kramer <.0001 0.05 1.3737 2.6649 0.9244 3.1142
donorgroup*region Autoab Pos 3_T Ins. neg. T1D 2_B 1.6472 0.3267 68 5.04 <.0001 Tukey-Kramer 0.0002 0.05 0.9954 2.2990 0.5417 2.7527
donorgroup*region Autoab Pos 3_T Ins. neg. T1D 3_T 1.1326 0.3817 68 2.97 0.0041 Tukey-Kramer 0.1414 0.05 0.3710 1.8942 -0.1591 2.4243
donorgroup*region Autoab Pos 3_T Ins. pos. T1D 1_H 1.7835 0.3060 68 5.83 <.0001 Tukey-Kramer <.0001 0.05 1.1728 2.3942 0.7477 2.8192
donorgroup*region Autoab Pos 3_T Ins. pos. T1D 2_B 1.7154 0.3084 68 5.56 <.0001 Tukey-Kramer <.0001 0.05 1.1001 2.3307 0.6718 2.7590
donorgroup*region Autoab Pos 3_T Ins. pos. T1D 3_T 1.2060 0.3498 68 3.45 0.0010 Tukey-Kramer 0.0421 0.05 0.5080 1.9040 0.02216 2.3899
donorgroup*region Autoab Pos 3_T No diabetes 1_H 0.4764 0.2938 68 1.62 0.1095 Tukey-Kramer 0.8950 0.05 -0.1099 1.0627 -0.5179 1.4708
donorgroup*region Autoab Pos 3_T No diabetes 2_B 0.4376 0.2969 68 1.47 0.1451 Tukey-Kramer 0.9426 0.05 -0.1548 1.0300 -0.5672 1.4423
donorgroup*region Autoab Pos 3_T No diabetes 3_T -0.4337 0.3268 68 -1.33 0.1890 Tukey-Kramer 0.9725 0.05 -1.0859 0.2185 -1.5398 0.6725
donorgroup*region Ins. neg. T1D 1_H Ins. neg. T1D 2_B -0.3721 0.1710 68 -2.18 0.0330 Tukey-Kramer 0.5717 0.05 -0.7133 -0.03094 -0.9508 0.2065
donorgroup*region Ins. neg. T1D 1_H Ins. neg. T1D 3_T -0.8867 0.2213 68 -4.01 0.0002 Tukey-Kramer 0.0079 0.05 -1.3283 -0.4452 -1.6357 -0.1378
donorgroup*region Ins. neg. T1D 1_H Ins. pos. T1D 1_H -0.2358 0.2497 68 -0.94 0.3484 Tukey-Kramer 0.9983 0.05 -0.7342 0.2625 -1.0810 0.6094
donorgroup*region Ins. neg. T1D 1_H Ins. pos. T1D 2_B -0.3039 0.2526 68 -1.20 0.2331 Tukey-Kramer 0.9870 0.05 -0.8079 0.2001 -1.1587 0.5509
donorgroup*region Ins. neg. T1D 1_H Ins. pos. T1D 3_T -0.8133 0.3018 68 -2.69 0.0089 Tukey-Kramer 0.2513 0.05 -1.4155 -0.2111 -1.8346 0.2081
donorgroup*region Ins. neg. T1D 1_H No diabetes 1_H -1.5429 0.2346 68 -6.58 <.0001 Tukey-Kramer <.0001 0.05 -2.0110 -1.0748 -2.3368 -0.7489
donorgroup*region Ins. neg. T1D 1_H No diabetes 2_B -1.5817 0.2384 68 -6.63 <.0001 Tukey-Kramer <.0001 0.05 -2.0575 -1.1060 -2.3886 -0.7748
donorgroup*region Ins. neg. T1D 1_H No diabetes 3_T -2.4530 0.2748 68 -8.93 <.0001 Tukey-Kramer <.0001 0.05 -3.0014 -1.9046 -3.3831 -1.5228
donorgroup*region Ins. neg. T1D 2_B Ins. neg. T1D 3_T -0.5146 0.2219 68 -2.32 0.0234 Tukey-Kramer 0.4734 0.05 -0.9573 -0.07193 -1.2654 0.2362
donorgroup*region Ins. neg. T1D 2_B Ins. pos. T1D 1_H 0.1363 0.2538 68 0.54 0.5929 Tukey-Kramer 1.0000 0.05 -0.3701 0.6427 -0.7226 0.9952
donorgroup*region Ins. neg. T1D 2_B Ins. pos. T1D 2_B 0.06822 0.2566 68 0.27 0.7911 Tukey-Kramer 1.0000 0.05 -0.4438 0.5802 -0.8001 0.9365
donorgroup*region Ins. neg. T1D 2_B Ins. pos. T1D 3_T -0.4412 0.3051 68 -1.45 0.1528 Tukey-Kramer 0.9496 0.05 -1.0500 0.1677 -1.4738 0.5915
donorgroup*region Ins. neg. T1D 2_B No diabetes 1_H -1.1707 0.2389 68 -4.90 <.0001 Tukey-Kramer 0.0004 0.05 -1.6474 -0.6941 -1.9792 -0.3623
donorgroup*region Ins. neg. T1D 2_B No diabetes 2_B -1.2096 0.2426 68 -4.98 <.0001 Tukey-Kramer 0.0003 0.05 -1.6938 -0.7254 -2.0308 -0.3884
donorgroup*region Ins. neg. T1D 2_B No diabetes 3_T -2.0808 0.2785 68 -7.47 <.0001 Tukey-Kramer <.0001 0.05 -2.6366 -1.5251 -3.0234 -1.1383
donorgroup*region Ins. neg. T1D 3_T Ins. pos. T1D 1_H 0.6509 0.3215 68 2.02 0.0468 Tukey-Kramer 0.6755 0.05 0.009352 1.2925 -0.4372 1.7391
donorgroup*region Ins. neg. T1D 3_T Ins. pos. T1D 2_B 0.5828 0.3237 68 1.80 0.0762 Tukey-Kramer 0.8120 0.05 -0.06314 1.2288 -0.5128 1.6784
donorgroup*region Ins. neg. T1D 3_T Ins. pos. T1D 3_T 0.07346 0.3634 68 0.20 0.8404 Tukey-Kramer 1.0000 0.05 -0.6517 0.7987 -1.1565 1.3034
donorgroup*region Ins. neg. T1D 3_T No diabetes 1_H -0.6561 0.3099 68 -2.12 0.0379 Tukey-Kramer 0.6126 0.05 -1.2745 -0.03774 -1.7049 0.3927
donorgroup*region Ins. neg. T1D 3_T No diabetes 2_B -0.6950 0.3128 68 -2.22 0.0296 Tukey-Kramer 0.5404 0.05 -1.3192 -0.07078 -1.7536 0.3637
donorgroup*region Ins. neg. T1D 3_T No diabetes 3_T -1.5662 0.3414 68 -4.59 <.0001 Tukey-Kramer 0.0011 0.05 -2.2474 -0.8850 -2.7216 -0.4109
donorgroup*region Ins. pos. T1D 1_H Ins. pos. T1D 2_B -0.06809 0.1431 68 -0.48 0.6356 Tukey-Kramer 1.0000 0.05 -0.3535 0.2174 -0.5522 0.4161
donorgroup*region Ins. pos. T1D 1_H Ins. pos. T1D 3_T -0.5775 0.1852 68 -3.12 0.0027 Tukey-Kramer 0.0990 0.05 -0.9469 -0.2080 -1.2041 0.04915
donorgroup*region Ins. pos. T1D 1_H No diabetes 1_H -1.3070 0.2098 68 -6.23 <.0001 Tukey-Kramer <.0001 0.05 -1.7257 -0.8884 -2.0172 -0.5969
donorgroup*region Ins. pos. T1D 1_H No diabetes 2_B -1.3459 0.2141 68 -6.29 <.0001 Tukey-Kramer <.0001 0.05 -1.7731 -0.9187 -2.0705 -0.6213
donorgroup*region Ins. pos. T1D 1_H No diabetes 3_T -2.2172 0.2540 68 -8.73 <.0001 Tukey-Kramer <.0001 0.05 -2.7240 -1.7103 -3.0769 -1.3575
donorgroup*region Ins. pos. T1D 2_B Ins. pos. T1D 3_T -0.5094 0.1856 68 -2.74 0.0077 Tukey-Kramer 0.2279 0.05 -0.8798 -0.1390 -1.1376 0.1188
donorgroup*region Ins. pos. T1D 2_B No diabetes 1_H -1.2390 0.2132 68 -5.81 <.0001 Tukey-Kramer <.0001 0.05 -1.6644 -0.8136 -1.9605 -0.5175
donorgroup*region Ins. pos. T1D 2_B No diabetes 2_B -1.2778 0.2174 68 -5.88 <.0001 Tukey-Kramer <.0001 0.05 -1.7116 -0.8440 -2.0136 -0.5421
donorgroup*region Ins. pos. T1D 2_B No diabetes 3_T -2.1491 0.2568 68 -8.37 <.0001 Tukey-Kramer <.0001 0.05 -2.6615 -1.6366 -3.0182 -1.2799
donorgroup*region Ins. pos. T1D 3_T No diabetes 1_H -0.7296 0.2697 68 -2.71 0.0086 Tukey-Kramer 0.2462 0.05 -1.2677 -0.1914 -1.6423 0.1831
donorgroup*region Ins. pos. T1D 3_T No diabetes 2_B -0.7684 0.2730 68 -2.81 0.0064 Tukey-Kramer 0.1974 0.05 -1.3132 -0.2236 -1.6924 0.1556
donorgroup*region Ins. pos. T1D 3_T No diabetes 3_T -1.6397 0.3053 68 -5.37 <.0001 Tukey-Kramer <.0001 0.05 -2.2490 -1.0304 -2.6731 -0.6063
donorgroup*region No diabetes 1_H No diabetes 2_B -0.03885 0.1241 68 -0.31 0.7553 Tukey-Kramer 1.0000 0.05 -0.2866 0.2089 -0.4590 0.3813
donorgroup*region No diabetes 1_H No diabetes 3_T -0.9101 0.1565 68 -5.82 <.0001 Tukey-Kramer <.0001 0.05 -1.2224 -0.5979 -1.4397 -0.3805
donorgroup*region No diabetes 2_B No diabetes 3_T -0.8713 0.1594 68 -5.47 <.0001 Tukey-Kramer <.0001 0.05 -1.1893 -0.5532 -1.4107 -0.3318

The SAS System

The PLM Procedure

The PLM Procedure

Store Information

Store Information
Item Store WORK.ENDOCRINE_MODEL_DATA
Data Set Created From WORK.CELL3
Created By PROC MIXED
Date Created 12NOV20:01:21:10
Response Variable percent_endocrine_area
Distribution Normal
Class Variables nPODCaseID donorgroup region
Model Effects Intercept region donorgroup donorgroup*region

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 1_H 2_B 3_T

Slices

donorgroup*region LS-Means

Slice of donorgroup*region Least Squares Means
Slice region Estimate Standard Error DF t Value Pr > |t| Alpha Lower Upper
donorgroup Autoab Pos 1_H 1.3770 0.1859 68 7.41 <.0001 0.05 1.0060 1.7479
donorgroup Autoab Pos 2_B 1.5376 0.1841 68 8.35 <.0001 0.05 1.1703 1.9049
donorgroup Autoab Pos 3_T 2.4773 0.2607 68 9.50 <.0001 0.05 1.9570 2.9976

donorgroup*region Diffs

Simple Differences of donorgroup*region Least Squares Means
Adjustment for Multiple Comparisons: Tukey-Kramer
Slice region region Estimate Standard Error DF t Value Pr > |t| Adj P Alpha Lower Upper Adj Lower Adj Upper
donorgroup Autoab Pos 1_H 2_B -0.1607 0.1674 68 -0.96 0.3406 0.6047 0.05 -0.4948 0.1734 -0.5618 0.2405
donorgroup Autoab Pos 1_H 3_T -1.1003 0.2128 68 -5.17 <.0001 <.0001 0.05 -1.5251 -0.6756 -1.6103 -0.5904
donorgroup Autoab Pos 2_B 3_T -0.9397 0.2075 68 -4.53 <.0001 <.0001 0.05 -1.3538 -0.5256 -1.4369 -0.4425

donorgroup*region LS-Means

Slice of donorgroup*region Least Squares Means
Slice region Estimate Standard Error DF t Value Pr > |t| Alpha Lower Upper
donorgroup Ins. neg. T1D 1_H 0.4580 0.1915 68 2.39 0.0196 0.05 0.07580 0.8402
donorgroup Ins. neg. T1D 2_B 0.8301 0.1968 68 4.22 <.0001 0.05 0.4375 1.2228
donorgroup Ins. neg. T1D 3_T 1.3448 0.2787 68 4.82 <.0001 0.05 0.7886 1.9010

donorgroup*region Diffs

Simple Differences of donorgroup*region Least Squares Means
Adjustment for Multiple Comparisons: Tukey-Kramer
Slice region region Estimate Standard Error DF t Value Pr > |t| Adj P Alpha Lower Upper Adj Lower Adj Upper
donorgroup Ins. neg. T1D 1_H 2_B -0.3721 0.1710 68 -2.18 0.0330 0.0826 0.05 -0.7133 -0.03094 -0.7818 0.03754
donorgroup Ins. neg. T1D 1_H 3_T -0.8867 0.2213 68 -4.01 0.0002 0.0005 0.05 -1.3283 -0.4452 -1.4170 -0.3565
donorgroup Ins. neg. T1D 2_B 3_T -0.5146 0.2219 68 -2.32 0.0234 0.0598 0.05 -0.9573 -0.07193 -1.0462 0.01693

donorgroup*region LS-Means

Slice of donorgroup*region Least Squares Means
Slice region Estimate Standard Error DF t Value Pr > |t| Alpha Lower Upper
donorgroup Ins. pos. T1D 1_H 0.6938 0.1603 68 4.33 <.0001 0.05 0.3740 1.0136
donorgroup Ins. pos. T1D 2_B 0.7619 0.1646 68 4.63 <.0001 0.05 0.4334 1.0904
donorgroup Ins. pos. T1D 3_T 1.2713 0.2332 68 5.45 <.0001 0.05 0.8059 1.7366

donorgroup*region Diffs

Simple Differences of donorgroup*region Least Squares Means
Adjustment for Multiple Comparisons: Tukey-Kramer
Slice region region Estimate Standard Error DF t Value Pr > |t| Adj P Alpha Lower Upper Adj Lower Adj Upper
donorgroup Ins. pos. T1D 1_H 2_B -0.06809 0.1431 68 -0.48 0.6356 0.8828 0.05 -0.3535 0.2174 -0.4108 0.2747
donorgroup Ins. pos. T1D 1_H 3_T -0.5775 0.1852 68 -3.12 0.0027 0.0074 0.05 -0.9469 -0.2080 -1.0211 -0.1338
donorgroup Ins. pos. T1D 2_B 3_T -0.5094 0.1856 68 -2.74 0.0077 0.0209 0.05 -0.8798 -0.1390 -0.9541 -0.06465

donorgroup*region LS-Means

Slice of donorgroup*region Least Squares Means
Slice region Estimate Standard Error DF t Value Pr > |t| Alpha Lower Upper
donorgroup No diabetes 1_H 2.0009 0.1354 68 14.77 <.0001 0.05 1.7306 2.2711
donorgroup No diabetes 2_B 2.0397 0.1420 68 14.37 <.0001 0.05 1.7564 2.3230
donorgroup No diabetes 3_T 2.9110 0.1971 68 14.77 <.0001 0.05 2.5177 3.3043

donorgroup*region Diffs

Simple Differences of donorgroup*region Least Squares Means
Adjustment for Multiple Comparisons: Tukey-Kramer
Slice region region Estimate Standard Error DF t Value Pr > |t| Adj P Alpha Lower Upper Adj Lower Adj Upper
donorgroup No diabetes 1_H 2_B -0.03885 0.1241 68 -0.31 0.7553 0.9475 0.05 -0.2866 0.2089 -0.3363 0.2586
donorgroup No diabetes 1_H 3_T -0.9101 0.1565 68 -5.82 <.0001 <.0001 0.05 -1.2224 -0.5979 -1.2850 -0.5352
donorgroup No diabetes 2_B 3_T -0.8713 0.1594 68 -5.47 <.0001 <.0001 0.05 -1.1893 -0.5532 -1.2532 -0.4894

Effect Plots

Statement 1

Interaction Plot 1

Interaction Plot for percent_endocrine_area by region categorized by donorgroup
In [119]:
%explore(percent_acinar_area);
Out[119]:
SAS Output

SAS Output

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable percent_acinar_area
Covariance Structure Variance Components
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method Parameter
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 1
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 664.70321058  
1 1 664.70321058 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
region nPODCaseI(donorgrou) 28.6855

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 664.7
AIC (Smaller is Better) 666.7
AICC (Smaller is Better) 666.7
BIC (Smaller is Better) 668.4

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
0 0.00 1.0000

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     76.6829 1.4314 35 53.57 <.0001
region   PB -0.7726 2.0629 68 -0.37 0.7092
region   PH -3.3002 2.0243 68 -1.63 0.1077
region   PT 0 . . . .
donorgroup Autoab Pos   1.8548 2.3737 35 0.78 0.4398
donorgroup Ins. neg. T1D   -12.1281 2.4793 35 -4.89 <.0001
donorgroup Ins. pos. T1D   0.6575 2.2175 35 0.30 0.7686
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB -1.1172 3.3804 68 -0.33 0.7421
donorgroup*region Autoab Pos PH -4.8738 3.4324 68 -1.42 0.1602
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB 7.0464 3.5287 68 2.00 0.0498
donorgroup*region Ins. neg. T1D PH 11.3752 3.5063 68 3.24 0.0018
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB -3.7599 3.1611 68 -1.19 0.2384
donorgroup*region Ins. pos. T1D PH -2.2783 3.1361 68 -0.73 0.4700
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 1.88 0.1600
donorgroup 3 35 6.48 0.0013
donorgroup*region 6 68 3.62 0.0036

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable percent_acinar_area
Covariance Structure Compound Symmetry
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method Profile
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 2
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 664.70321058  
1 2 647.06583645 0.00000010
2 1 647.06581400 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
CS nPODCaseI(donorgrou) 12.3828
Residual   16.2060

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 647.1
AIC (Smaller is Better) 651.1
AICC (Smaller is Better) 651.2
BIC (Smaller is Better) 654.4

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
1 17.64 <.0001

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     76.6829 1.4290 35 53.66 <.0001
region   PB -0.8204 1.5592 68 -0.53 0.6005
region   PH -3.3002 1.5216 68 -2.17 0.0336
region   PT 0 . . . .
donorgroup Autoab Pos   1.8548 2.3697 35 0.78 0.4391
donorgroup Ins. neg. T1D   -12.1281 2.4751 35 -4.90 <.0001
donorgroup Ins. pos. T1D   0.6575 2.2138 35 0.30 0.7682
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB -1.0694 2.5461 68 -0.42 0.6758
donorgroup*region Autoab Pos PH -4.5876 2.5968 68 -1.77 0.0818
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB 7.0942 2.6573 68 2.67 0.0095
donorgroup*region Ins. neg. T1D PH 11.3752 2.6354 68 4.32 <.0001
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB -3.7121 2.3817 68 -1.56 0.1237
donorgroup*region Ins. pos. T1D PH -2.2783 2.3572 68 -0.97 0.3372
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 3.07 0.0527
donorgroup 3 35 3.53 0.0247
donorgroup*region 6 68 6.23 <.0001

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable percent_acinar_area
Covariance Structure Unstructured
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 6
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 664.70321058  
1 2 646.73601230 0.00000007
2 1 646.73599684 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
UN(1,1) nPODCaseI(donorgrou) 30.0532
UN(2,1) nPODCaseI(donorgrou) 11.3253
UN(2,2) nPODCaseI(donorgrou) 27.9895
UN(3,1) nPODCaseI(donorgrou) 13.1060
UN(3,2) nPODCaseI(donorgrou) 12.6297
UN(3,3) nPODCaseI(donorgrou) 27.7154

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 646.7
AIC (Smaller is Better) 658.7
AICC (Smaller is Better) 659.6
BIC (Smaller is Better) 668.7

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
5 17.97 0.0030

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     76.6829 1.4070 35 54.50 <.0001
region   PB -0.8141 1.5421 35 -0.53 0.6009
region   PH -3.3002 1.4747 35 -2.24 0.0317
region   PT 0 . . . .
donorgroup Autoab Pos   1.8548 2.3333 35 0.79 0.4320
donorgroup Ins. neg. T1D   -12.1281 2.4370 35 -4.98 <.0001
donorgroup Ins. pos. T1D   0.6575 2.1797 35 0.30 0.7647
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB -1.0757 2.5145 35 -0.43 0.6714
donorgroup*region Autoab Pos PH -4.6419 2.5211 35 -1.84 0.0741
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB 7.0879 2.6241 35 2.70 0.0106
donorgroup*region Ins. neg. T1D PH 11.3752 2.5542 35 4.45 <.0001
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB -3.7184 2.3524 35 -1.58 0.1229
donorgroup*region Ins. pos. T1D PH -2.2783 2.2846 35 -1.00 0.3255
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 35 3.11 0.0571
donorgroup 3 35 3.52 0.0248
donorgroup*region 6 35 6.73 <.0001

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable percent_acinar_area
Covariance Structure Unstructured using Correlations
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 6
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 664.70321058  
1 2 646.73600709 0.00000004
2 1 646.73599684 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 30.0532
Var(2) nPODCaseI(donorgrou) 27.9895
Var(3) nPODCaseI(donorgrou) 27.7154
Corr(2,1) nPODCaseI(donorgrou) 0.3905
Corr(3,1) nPODCaseI(donorgrou) 0.4541
Corr(3,2) nPODCaseI(donorgrou) 0.4535

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 646.7
AIC (Smaller is Better) 658.7
AICC (Smaller is Better) 659.6
BIC (Smaller is Better) 668.7

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
5 17.97 0.0030

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     76.6829 1.4070 35 54.50 <.0001
region   PB -0.8141 1.5421 35 -0.53 0.6009
region   PH -3.3002 1.4747 35 -2.24 0.0317
region   PT 0 . . . .
donorgroup Autoab Pos   1.8548 2.3333 35 0.79 0.4320
donorgroup Ins. neg. T1D   -12.1281 2.4370 35 -4.98 <.0001
donorgroup Ins. pos. T1D   0.6575 2.1797 35 0.30 0.7647
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB -1.0757 2.5145 35 -0.43 0.6714
donorgroup*region Autoab Pos PH -4.6419 2.5211 35 -1.84 0.0741
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB 7.0879 2.6241 35 2.70 0.0106
donorgroup*region Ins. neg. T1D PH 11.3752 2.5542 35 4.45 <.0001
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB -3.7184 2.3524 35 -1.58 0.1229
donorgroup*region Ins. pos. T1D PH -2.2783 2.2846 35 -1.00 0.3255
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 35 3.11 0.0571
donorgroup 3 35 3.52 0.0248
donorgroup*region 6 35 6.73 <.0001

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable percent_acinar_area
Covariance Structure Banded
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 6
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 45 664.70321058  
1 44 3170.60627529 0.46976519
2 44 3170.60627529 0.46976519

Convergence Status

WARNING: Stopped because of too many likelihood evaluations.

Covariance Parameter Values At Last Iteration

Covariance Parameter Values At Last Iteration
Cov Parm Subject Estimate
UN(1,1) nPODCaseI(donorgrou) 1.0000
UN(2,1) nPODCaseI(donorgrou) 0
UN(2,2) nPODCaseI(donorgrou) 1.0000
UN(3,1) nPODCaseI(donorgrou) 0
UN(3,2) nPODCaseI(donorgrou) 0
UN(3,3) nPODCaseI(donorgrou) 1.0000

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable percent_acinar_area
Covariance Structure Heterogeneous Compound Symmetry
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 4
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 664.70321058  
1 2 646.94932591 0.00000003
2 1 646.94931833 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 30.2466
Var(2) nPODCaseI(donorgrou) 28.2104
Var(3) nPODCaseI(donorgrou) 27.3546
CSH nPODCaseI(donorgrou) 0.4336

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 646.9
AIC (Smaller is Better) 654.9
AICC (Smaller is Better) 655.4
BIC (Smaller is Better) 661.6

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
3 17.75 0.0005

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     76.6829 1.3978 35 54.86 <.0001
region   PB -0.8222 1.5670 68 -0.52 0.6015
region   PH -3.3002 1.4995 68 -2.20 0.0311
region   PT 0 . . . .
donorgroup Autoab Pos   1.8548 2.3180 35 0.80 0.4290
donorgroup Ins. neg. T1D   -12.1281 2.4211 35 -5.01 <.0001
donorgroup Ins. pos. T1D   0.6575 2.1655 35 0.30 0.7632
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB -1.0675 2.5569 68 -0.42 0.6776
donorgroup*region Autoab Pos PH -4.5949 2.5602 68 -1.79 0.0771
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB 7.0961 2.6685 68 2.66 0.0098
donorgroup*region Ins. neg. T1D PH 11.3752 2.5971 68 4.38 <.0001
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB -3.7102 2.3919 68 -1.55 0.1255
donorgroup*region Ins. pos. T1D PH -2.2783 2.3229 68 -0.98 0.3302
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 3.12 0.0504
donorgroup 3 35 3.52 0.0248
donorgroup*region 6 68 6.40 <.0001

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable percent_acinar_area
Covariance Structure Huynh-Feldt
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 4
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 664.70321058  
1 2 647.02791470 0.00000005
2 1 647.02790319 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 29.2910
Var(2) nPODCaseI(donorgrou) 27.7721
Var(3) nPODCaseI(donorgrou) 28.6901
HF nPODCaseI(donorgrou) 16.2067

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 647.0
AIC (Smaller is Better) 655.0
AICC (Smaller is Better) 655.4
BIC (Smaller is Better) 661.7

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
3 17.68 0.0005

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     76.6829 1.4315 35 53.57 <.0001
region   PB -0.8213 1.5599 68 -0.53 0.6002
region   PH -3.3002 1.5216 68 -2.17 0.0336
region   PT 0 . . . .
donorgroup Autoab Pos   1.8548 2.3739 35 0.78 0.4399
donorgroup Ins. neg. T1D   -12.1281 2.4795 35 -4.89 <.0001
donorgroup Ins. pos. T1D   0.6575 2.2177 35 0.30 0.7686
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB -1.0684 2.5465 68 -0.42 0.6761
donorgroup*region Autoab Pos PH -4.5954 2.5954 68 -1.77 0.0811
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB 7.0952 2.6578 68 2.67 0.0095
donorgroup*region Ins. neg. T1D PH 11.3752 2.6355 68 4.32 <.0001
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB -3.7111 2.3821 68 -1.56 0.1239
donorgroup*region Ins. pos. T1D PH -2.2783 2.3572 68 -0.97 0.3372
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 3.08 0.0524
donorgroup 3 35 3.53 0.0247
donorgroup*region 6 68 6.24 <.0001

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable percent_acinar_area
Covariance Structure Heterogeneous Autoregressive
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 4
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 664.70321058  
1 2 651.04837508 0.00000002
2 1 651.04837079 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 30.5578
Var(2) nPODCaseI(donorgrou) 28.0325
Var(3) nPODCaseI(donorgrou) 27.3351
ARH(1) nPODCaseI(donorgrou) 0.4243

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 651.0
AIC (Smaller is Better) 659.0
AICC (Smaller is Better) 659.5
BIC (Smaller is Better) 665.7

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
3 13.65 0.0034

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     76.6829 1.3973 35 54.88 <.0001
region   PB -0.8302 1.8787 68 -0.44 0.6600
region   PH -3.3002 1.5089 68 -2.19 0.0322
region   PT 0 . . . .
donorgroup Autoab Pos   1.8548 2.3172 35 0.80 0.4288
donorgroup Ins. neg. T1D   -12.1281 2.4202 35 -5.01 <.0001
donorgroup Ins. pos. T1D   0.6575 2.1647 35 0.30 0.7631
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB -1.0595 3.0765 68 -0.34 0.7316
donorgroup*region Autoab Pos PH -4.5446 2.5708 68 -1.77 0.0816
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB 7.1040 3.2114 68 2.21 0.0303
donorgroup*region Ins. neg. T1D PH 11.3752 2.6135 68 4.35 <.0001
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB -3.7023 2.8771 68 -1.29 0.2025
donorgroup*region Ins. pos. T1D PH -2.2783 2.3376 68 -0.97 0.3332
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 3.52 0.0351
donorgroup 3 35 3.90 0.0166
donorgroup*region 6 68 6.12 <.0001

The SAS System

The PRINT Procedure

Data Set WORK.ALL

Description arh1 cs csh hf un unr vc
-2 Res Log Likelihood 651.0 647.1 646.9 647.0 646.7 646.7 664.7
AIC (Smaller is Better) 659.0 651.1 654.9 655.0 658.7 658.7 666.7
AICC (Smaller is Better) 659.5 651.2 655.4 655.4 659.6 659.6 666.7
BIC (Smaller is Better) 665.7 654.4 661.6 661.7 668.7 668.7 668.4

The SAS System

The PRINT Procedure

Data Set WORK.STATUS

Obs Reason Status pdG pdH covar
1 Convergence criteria met. 0 1 1 arh(1)
2 Convergence criteria met. 0 1 1 cs
3 Convergence criteria met. 0 1 1 csh
4 Convergence criteria met. 0 1 1 hf
5 Convergence criteria met. 0 1 1 un
6 WARNING: Stopped because of too many likelihood evaluations. 1 1 1 un1
7 Convergence criteria met. 0 1 1 unr
8 Convergence criteria met. 0 1 1 vc
In [120]:
PROC mixed data=cell3 /*maxiter=1000 maxfunc=5000  can also use covtest*/;
format region $regionformat.;
     class nPODCaseID donorgroup region;
     model  percent_acinar_area =region|donorgroup/solution; /*can use  ddfm = kenwardroger after solution for unbalanced data to improve performance of t and f tests*/
     /*option e3 after solution helps to describe how type 3 tests were constructed*/
     repeated  region/ subject=nPODCaseID(donorgroup) type=un; 
     lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;
     store acinar_model_data;
run;

/*for interaction term, reporting lsmeans and SE vs arithmetic means and SD, since not all data is balanced;
however, lsmeans and arithemic means are largely identical when data not missing

PROC means data=cell3 n mean std ;
class donorgroup region;
types () donorgroup*region;
var percent_acinar_area;
run;
*/


proc plm restore=acinar_model_data;
effectplot interaction(sliceby=donorgroup);
slice donorgroup*region/sliceby=donorgroup diff adjust=tukey cl pdiff alpha=0.05 plots=none nof means;
run;
Out[120]:
SAS Output

SAS Output

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable percent_acinar_area
Covariance Structure Unstructured
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 1_H 2_B 3_T

Dimensions

Dimensions
Covariance Parameters 6
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 664.70321058  
1 2 646.73601230 0.00000007
2 1 646.73599684 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
UN(1,1) nPODCaseI(donorgrou) 27.9895
UN(2,1) nPODCaseI(donorgrou) 11.3253
UN(2,2) nPODCaseI(donorgrou) 30.0532
UN(3,1) nPODCaseI(donorgrou) 12.6297
UN(3,2) nPODCaseI(donorgrou) 13.1060
UN(3,3) nPODCaseI(donorgrou) 27.7154

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 646.7
AIC (Smaller is Better) 658.7
AICC (Smaller is Better) 659.6
BIC (Smaller is Better) 668.7

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
5 17.97 0.0030

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     76.6829 1.4070 35 54.50 <.0001
region   1_H -3.3002 1.4747 35 -2.24 0.0317
region   2_B -0.8141 1.5421 35 -0.53 0.6009
region   3_T 0 . . . .
donorgroup Autoab Pos   1.8548 2.3333 35 0.79 0.4320
donorgroup Ins. neg. T1D   -12.1281 2.4370 35 -4.98 <.0001
donorgroup Ins. pos. T1D   0.6575 2.1797 35 0.30 0.7647
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos 1_H -4.6419 2.5211 35 -1.84 0.0741
donorgroup*region Autoab Pos 2_B -1.0757 2.5145 35 -0.43 0.6714
donorgroup*region Autoab Pos 3_T 0 . . . .
donorgroup*region Ins. neg. T1D 1_H 11.3752 2.5542 35 4.45 <.0001
donorgroup*region Ins. neg. T1D 2_B 7.0879 2.6241 35 2.70 0.0106
donorgroup*region Ins. neg. T1D 3_T 0 . . . .
donorgroup*region Ins. pos. T1D 1_H -2.2783 2.2846 35 -1.00 0.3255
donorgroup*region Ins. pos. T1D 2_B -3.7184 2.3524 35 -1.58 0.1229
donorgroup*region Ins. pos. T1D 3_T 0 . . . .
donorgroup*region No diabetes 1_H 0 . . . .
donorgroup*region No diabetes 2_B 0 . . . .
donorgroup*region No diabetes 3_T 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 35 3.11 0.0571
donorgroup 3 35 3.52 0.0248
donorgroup*region 6 35 6.73 <.0001

Least Squares Means

Least Squares Means
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t| Alpha Lower Upper
region   1_H 72.0925 0.8899 35 81.01 <.0001 0.05 70.2859 73.8991
region   2_B 74.0383 0.9126 35 81.13 <.0001 0.05 72.1856 75.8911
region   3_T 74.2790 0.8723 35 85.15 <.0001 0.05 72.5081 76.0499
donorgroup Autoab Pos   75.2604 1.5041 35 50.04 <.0001 0.05 72.2070 78.3139
donorgroup Ins. neg. T1D   69.3378 1.5930 35 43.53 <.0001 0.05 66.1037 72.5718
donorgroup Ins. pos. T1D   73.9700 1.3328 35 55.50 <.0001 0.05 71.2642 76.6758
donorgroup No diabetes   75.3115 1.1325 35 66.50 <.0001 0.05 73.0123 77.6107
donorgroup*region Autoab Pos 1_H 70.5956 1.9683 35 35.87 <.0001 0.05 66.5997 74.5915
donorgroup*region Autoab Pos 2_B 76.6480 1.9382 35 39.55 <.0001 0.05 72.7132 80.5828
donorgroup*region Autoab Pos 3_T 78.5377 1.8613 35 42.20 <.0001 0.05 74.7591 82.3164
donorgroup*region Ins. neg. T1D 1_H 72.6299 1.9996 35 36.32 <.0001 0.05 68.5704 76.6893
donorgroup*region Ins. neg. T1D 2_B 70.8287 2.0720 35 34.18 <.0001 0.05 66.6222 75.0351
donorgroup*region Ins. neg. T1D 3_T 64.5548 1.9898 35 32.44 <.0001 0.05 60.5153 68.5944
donorgroup*region Ins. pos. T1D 1_H 71.7618 1.6730 35 42.89 <.0001 0.05 68.3654 75.1582
donorgroup*region Ins. pos. T1D 2_B 72.8079 1.7336 35 42.00 <.0001 0.05 69.2885 76.3273
donorgroup*region Ins. pos. T1D 3_T 77.3404 1.6648 35 46.46 <.0001 0.05 73.9606 80.7201
donorgroup*region No diabetes 1_H 73.3827 1.4139 35 51.90 <.0001 0.05 70.5122 76.2532
donorgroup*region No diabetes 2_B 75.8688 1.5069 35 50.35 <.0001 0.05 72.8097 78.9279
donorgroup*region No diabetes 3_T 76.6829 1.4070 35 54.50 <.0001 0.05 73.8265 79.5393

Differences of Least Squares Means

Differences of Least Squares Means
Effect donorgroup region _donorgroup region Estimate Standard
Error
DF t Value Pr > |t| Adjustment Adj P Alpha Lower Upper Adj Lower Adj Upper
region   1_H   2_B -1.9459 1.0015 35 -1.94 0.0601 Tukey-Kramer 0.1418 0.05 -3.9789 0.08722 -4.3967 0.5050
region   1_H   3_T -2.1865 0.9270 35 -2.36 0.0241 Tukey-Kramer 0.0608 0.05 -4.0684 -0.3045 -4.4551 0.08221
region   2_B   3_T -0.2406 0.9350 35 -0.26 0.7984 Tukey-Kramer 0.9642 0.05 -2.1387 1.6575 -2.5287 2.0475
donorgroup Autoab Pos   Ins. neg. T1D   5.9227 2.1909 35 2.70 0.0105 Tukey-Kramer 0.0493 0.05 1.4749 10.3704 0.01401 11.8313
donorgroup Autoab Pos   Ins. pos. T1D   1.2904 2.0097 35 0.64 0.5250 Tukey-Kramer 0.9176 0.05 -2.7894 5.3703 -4.1294 6.7103
donorgroup Autoab Pos   No diabetes   -0.05102 1.8828 35 -0.03 0.9785 Tukey-Kramer 1.0000 0.05 -3.8733 3.7713 -5.1288 5.0267
donorgroup Ins. neg. T1D   Ins. pos. T1D   -4.6322 2.0771 35 -2.23 0.0322 Tukey-Kramer 0.1350 0.05 -8.8489 -0.4156 -10.2339 0.9694
donorgroup Ins. neg. T1D   No diabetes   -5.9737 1.9546 35 -3.06 0.0043 Tukey-Kramer 0.0212 0.05 -9.9417 -2.0056 -11.2450 -0.7023
donorgroup Ins. pos. T1D   No diabetes   -1.3414 1.7490 35 -0.77 0.4482 Tukey-Kramer 0.8687 0.05 -4.8922 2.2093 -6.0584 3.3755
donorgroup*region Autoab Pos 1_H Autoab Pos 2_B -6.0524 2.1908 35 -2.76 0.0091 Tukey-Kramer 0.2394 0.05 -10.5000 -1.6048 -13.7133 1.6085
donorgroup*region Autoab Pos 1_H Autoab Pos 3_T -7.9421 2.0448 35 -3.88 0.0004 Tukey-Kramer 0.0190 0.05 -12.0933 -3.7909 -15.0925 -0.7917
donorgroup*region Autoab Pos 1_H Ins. neg. T1D 1_H -2.0343 2.8058 35 -0.73 0.4733 Tukey-Kramer 0.9998 0.05 -7.7304 3.6619 -11.8458 7.7773
donorgroup*region Autoab Pos 1_H Ins. neg. T1D 2_B -0.2331 2.8579 35 -0.08 0.9355 Tukey-Kramer 1.0000 0.05 -6.0349 5.5688 -10.2267 9.7605
donorgroup*region Autoab Pos 1_H Ins. neg. T1D 3_T 6.0408 2.7989 35 2.16 0.0378 Tukey-Kramer 0.5877 0.05 0.3588 11.7228 -3.7464 15.8279
donorgroup*region Autoab Pos 1_H Ins. pos. T1D 1_H -1.1662 2.5833 35 -0.45 0.6544 Tukey-Kramer 1.0000 0.05 -6.4105 4.0781 -10.1995 7.8670
donorgroup*region Autoab Pos 1_H Ins. pos. T1D 2_B -2.2123 2.6229 35 -0.84 0.4047 Tukey-Kramer 0.9993 0.05 -7.5371 3.1125 -11.3841 6.9595
donorgroup*region Autoab Pos 1_H Ins. pos. T1D 3_T -6.7448 2.5779 35 -2.62 0.0130 Tukey-Kramer 0.3091 0.05 -11.9783 -1.5112 -15.7594 2.2699
donorgroup*region Autoab Pos 1_H No diabetes 1_H -2.7871 2.4235 35 -1.15 0.2579 Tukey-Kramer 0.9896 0.05 -7.7071 2.1329 -11.2618 5.6876
donorgroup*region Autoab Pos 1_H No diabetes 2_B -5.2732 2.4789 35 -2.13 0.0405 Tukey-Kramer 0.6081 0.05 -10.3056 -0.2408 -13.9415 3.3951
donorgroup*region Autoab Pos 1_H No diabetes 3_T -6.0873 2.4195 35 -2.52 0.0166 Tukey-Kramer 0.3634 0.05 -10.9991 -1.1755 -14.5479 2.3733
donorgroup*region Autoab Pos 2_B Autoab Pos 3_T -1.8897 1.9861 35 -0.95 0.3479 Tukey-Kramer 0.9979 0.05 -5.9217 2.1423 -8.8348 5.0553
donorgroup*region Autoab Pos 2_B Ins. neg. T1D 1_H 4.0182 2.7848 35 1.44 0.1579 Tukey-Kramer 0.9460 0.05 -1.6353 9.6716 -5.7199 13.7562
donorgroup*region Autoab Pos 2_B Ins. neg. T1D 2_B 5.8193 2.8372 35 2.05 0.0478 Tukey-Kramer 0.6578 0.05 0.05943 11.5793 -4.1020 15.7407
donorgroup*region Autoab Pos 2_B Ins. neg. T1D 3_T 12.0932 2.7778 35 4.35 0.0001 Tukey-Kramer 0.0054 0.05 6.4540 17.7323 2.3798 21.8066
donorgroup*region Autoab Pos 2_B Ins. pos. T1D 1_H 4.8862 2.5604 35 1.91 0.0646 Tukey-Kramer 0.7464 0.05 -0.3117 10.0841 -4.0671 13.8394
donorgroup*region Autoab Pos 2_B Ins. pos. T1D 2_B 3.8401 2.6004 35 1.48 0.1487 Tukey-Kramer 0.9373 0.05 -1.4389 9.1192 -5.2530 12.9332
donorgroup*region Autoab Pos 2_B Ins. pos. T1D 3_T -0.6924 2.5550 35 -0.27 0.7880 Tukey-Kramer 1.0000 0.05 -5.8793 4.4946 -9.6269 8.2422
donorgroup*region Autoab Pos 2_B No diabetes 1_H 3.2653 2.3991 35 1.36 0.1822 Tukey-Kramer 0.9636 0.05 -1.6052 8.1358 -5.1241 11.6547
donorgroup*region Autoab Pos 2_B No diabetes 2_B 0.7792 2.4551 35 0.32 0.7528 Tukey-Kramer 1.0000 0.05 -4.2048 5.7632 -7.8057 9.3641
donorgroup*region Autoab Pos 2_B No diabetes 3_T -0.03490 2.3951 35 -0.01 0.9885 Tukey-Kramer 1.0000 0.05 -4.8971 4.8273 -8.4100 8.3402
donorgroup*region Autoab Pos 3_T Ins. neg. T1D 1_H 5.9079 2.7318 35 2.16 0.0375 Tukey-Kramer 0.5849 0.05 0.3620 11.4538 -3.6449 15.4607
donorgroup*region Autoab Pos 3_T Ins. neg. T1D 2_B 7.7091 2.7853 35 2.77 0.0090 Tukey-Kramer 0.2372 0.05 2.0547 13.3635 -2.0306 17.4487
donorgroup*region Autoab Pos 3_T Ins. neg. T1D 3_T 13.9829 2.7247 35 5.13 <.0001 Tukey-Kramer 0.0006 0.05 8.4516 19.5143 4.4552 23.5106
donorgroup*region Autoab Pos 3_T Ins. pos. T1D 1_H 6.7759 2.5027 35 2.71 0.0104 Tukey-Kramer 0.2643 0.05 1.6952 11.8566 -1.9755 15.5274
donorgroup*region Autoab Pos 3_T Ins. pos. T1D 2_B 5.7298 2.5436 35 2.25 0.0307 Tukey-Kramer 0.5257 0.05 0.5661 10.8936 -3.1646 14.6243
donorgroup*region Autoab Pos 3_T Ins. pos. T1D 3_T 1.1974 2.4972 35 0.48 0.6346 Tukey-Kramer 1.0000 0.05 -3.8722 6.2669 -7.5349 9.9296
donorgroup*region Autoab Pos 3_T No diabetes 1_H 5.1550 2.3375 35 2.21 0.0341 Tukey-Kramer 0.5567 0.05 0.4098 9.9003 -3.0186 13.3287
donorgroup*region Autoab Pos 3_T No diabetes 2_B 2.6689 2.3948 35 1.11 0.2727 Tukey-Kramer 0.9919 0.05 -2.1928 7.5306 -5.7053 11.0431
donorgroup*region Autoab Pos 3_T No diabetes 3_T 1.8548 2.3333 35 0.79 0.4320 Tukey-Kramer 0.9996 0.05 -2.8819 6.5916 -6.3042 10.0139
donorgroup*region Ins. neg. T1D 1_H Ins. neg. T1D 2_B 1.8012 2.2486 35 0.80 0.4285 Tukey-Kramer 0.9996 0.05 -2.7636 6.3660 -6.0616 9.6640
donorgroup*region Ins. neg. T1D 1_H Ins. neg. T1D 3_T 8.0750 2.0855 35 3.87 0.0005 Tukey-Kramer 0.0196 0.05 3.8412 12.3088 0.7823 15.3677
donorgroup*region Ins. neg. T1D 1_H Ins. pos. T1D 1_H 0.8680 2.6072 35 0.33 0.7412 Tukey-Kramer 1.0000 0.05 -4.4248 6.1609 -8.2489 9.9850
donorgroup*region Ins. neg. T1D 1_H Ins. pos. T1D 2_B -0.1780 2.6465 35 -0.07 0.9467 Tukey-Kramer 1.0000 0.05 -5.5507 5.1946 -9.4323 9.0762
donorgroup*region Ins. neg. T1D 1_H Ins. pos. T1D 3_T -4.7105 2.6019 35 -1.81 0.0788 Tukey-Kramer 0.8017 0.05 -9.9927 0.5717 -13.8090 4.3880
donorgroup*region Ins. neg. T1D 1_H No diabetes 1_H -0.7528 2.4490 35 -0.31 0.7604 Tukey-Kramer 1.0000 0.05 -5.7246 4.2190 -9.3167 7.8110
donorgroup*region Ins. neg. T1D 1_H No diabetes 2_B -3.2390 2.5038 35 -1.29 0.2043 Tukey-Kramer 0.9746 0.05 -8.3220 1.8441 -11.9944 5.5165
donorgroup*region Ins. neg. T1D 1_H No diabetes 3_T -4.0530 2.4450 35 -1.66 0.1063 Tukey-Kramer 0.8748 0.05 -9.0167 0.9106 -12.6029 4.4968
donorgroup*region Ins. neg. T1D 2_B Ins. neg. T1D 3_T 6.2738 2.1232 35 2.95 0.0056 Tukey-Kramer 0.1658 0.05 1.9635 10.5842 -1.1507 13.6984
donorgroup*region Ins. neg. T1D 2_B Ins. pos. T1D 1_H -0.9332 2.6631 35 -0.35 0.7281 Tukey-Kramer 1.0000 0.05 -6.3396 4.4733 -10.2457 8.3794
donorgroup*region Ins. neg. T1D 2_B Ins. pos. T1D 2_B -1.9792 2.7016 35 -0.73 0.4687 Tukey-Kramer 0.9998 0.05 -7.4638 3.5053 -11.4263 7.4678
donorgroup*region Ins. neg. T1D 2_B Ins. pos. T1D 3_T -6.5117 2.6580 35 -2.45 0.0194 Tukey-Kramer 0.4018 0.05 -11.9077 -1.1157 -15.8062 2.7828
donorgroup*region Ins. neg. T1D 2_B No diabetes 1_H -2.5540 2.5085 35 -1.02 0.3156 Tukey-Kramer 0.9962 0.05 -7.6466 2.5385 -11.3258 6.2178
donorgroup*region Ins. neg. T1D 2_B No diabetes 2_B -5.0402 2.5620 35 -1.97 0.0571 Tukey-Kramer 0.7108 0.05 -10.2413 0.1610 -13.9991 3.9188
donorgroup*region Ins. neg. T1D 2_B No diabetes 3_T -5.8542 2.5046 35 -2.34 0.0253 Tukey-Kramer 0.4711 0.05 -10.9388 -0.7696 -14.6124 2.9039
donorgroup*region Ins. neg. T1D 3_T Ins. pos. T1D 1_H -7.2070 2.5997 35 -2.77 0.0089 Tukey-Kramer 0.2352 0.05 -12.4846 -1.9294 -16.2976 1.8836
donorgroup*region Ins. neg. T1D 3_T Ins. pos. T1D 2_B -8.2531 2.6391 35 -3.13 0.0035 Tukey-Kramer 0.1159 0.05 -13.6107 -2.8955 -17.4814 0.9753
donorgroup*region Ins. neg. T1D 3_T Ins. pos. T1D 3_T -12.7855 2.5944 35 -4.93 <.0001 Tukey-Kramer 0.0011 0.05 -18.0524 -7.5186 -21.8577 -3.7134
donorgroup*region Ins. neg. T1D 3_T No diabetes 1_H -8.8279 2.4410 35 -3.62 0.0009 Tukey-Kramer 0.0374 0.05 -13.7834 -3.8723 -17.3637 -0.2920
donorgroup*region Ins. neg. T1D 3_T No diabetes 2_B -11.3140 2.4960 35 -4.53 <.0001 Tukey-Kramer 0.0033 0.05 -16.3811 -6.2468 -20.0421 -2.5859
donorgroup*region Ins. neg. T1D 3_T No diabetes 3_T -12.1281 2.4370 35 -4.98 <.0001 Tukey-Kramer 0.0009 0.05 -17.0755 -7.1807 -20.6499 -3.6063
donorgroup*region Ins. pos. T1D 1_H Ins. pos. T1D 2_B -1.0461 1.8813 35 -0.56 0.5817 Tukey-Kramer 1.0000 0.05 -4.8653 2.7731 -7.6246 5.5324
donorgroup*region Ins. pos. T1D 1_H Ins. pos. T1D 3_T -5.5785 1.7449 35 -3.20 0.0029 Tukey-Kramer 0.0996 0.05 -9.1208 -2.0363 -11.6801 0.5230
donorgroup*region Ins. pos. T1D 1_H No diabetes 1_H -1.6209 2.1905 35 -0.74 0.4643 Tukey-Kramer 0.9998 0.05 -6.0678 2.8260 -9.2806 6.0389
donorgroup*region Ins. pos. T1D 1_H No diabetes 2_B -4.1070 2.2516 35 -1.82 0.0767 Tukey-Kramer 0.7943 0.05 -8.6779 0.4639 -11.9804 3.7664
donorgroup*region Ins. pos. T1D 1_H No diabetes 3_T -4.9211 2.1860 35 -2.25 0.0308 Tukey-Kramer 0.5267 0.05 -9.3589 -0.4833 -12.5652 2.7230
donorgroup*region Ins. pos. T1D 2_B Ins. pos. T1D 3_T -4.5325 1.7764 35 -2.55 0.0153 Tukey-Kramer 0.3436 0.05 -8.1388 -0.9261 -10.7443 1.6794
donorgroup*region Ins. pos. T1D 2_B No diabetes 1_H -0.5748 2.2371 35 -0.26 0.7987 Tukey-Kramer 1.0000 0.05 -5.1163 3.9667 -8.3975 7.2479
donorgroup*region Ins. pos. T1D 2_B No diabetes 2_B -3.0609 2.2969 35 -1.33 0.1913 Tukey-Kramer 0.9686 0.05 -7.7240 1.6021 -11.0930 4.9711
donorgroup*region Ins. pos. T1D 2_B No diabetes 3_T -3.8750 2.2327 35 -1.74 0.0914 Tukey-Kramer 0.8397 0.05 -8.4076 0.6576 -11.6824 3.9324
donorgroup*region Ins. pos. T1D 3_T No diabetes 1_H 3.9577 2.1842 35 1.81 0.0786 Tukey-Kramer 0.8008 0.05 -0.4765 8.3919 -3.6802 11.5955
donorgroup*region Ins. pos. T1D 3_T No diabetes 2_B 1.4715 2.2455 35 0.66 0.5165 Tukey-Kramer 0.9999 0.05 -3.0870 6.0301 -6.3805 9.3236
donorgroup*region Ins. pos. T1D 3_T No diabetes 3_T 0.6575 2.1797 35 0.30 0.7647 Tukey-Kramer 1.0000 0.05 -3.7676 5.0825 -6.9647 8.2796
donorgroup*region No diabetes 1_H No diabetes 2_B -2.4861 1.6285 35 -1.53 0.1358 Tukey-Kramer 0.9227 0.05 -5.7921 0.8199 -8.1807 3.2085
donorgroup*region No diabetes 1_H No diabetes 3_T -3.3002 1.4747 35 -2.24 0.0317 Tukey-Kramer 0.5354 0.05 -6.2940 -0.3064 -8.4569 1.8565
donorgroup*region No diabetes 2_B No diabetes 3_T -0.8141 1.5421 35 -0.53 0.6009 Tukey-Kramer 1.0000 0.05 -3.9447 2.3165 -6.2065 4.5783

The SAS System

The PLM Procedure

The PLM Procedure

Store Information

Store Information
Item Store WORK.ACINAR_MODEL_DATA
Data Set Created From WORK.CELL3
Created By PROC MIXED
Date Created 12NOV20:01:21:13
Response Variable percent_acinar_area
Distribution Normal
Class Variables nPODCaseID donorgroup region
Model Effects Intercept region donorgroup donorgroup*region

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 1_H 2_B 3_T

Slices

donorgroup*region LS-Means

Slice of donorgroup*region Least Squares Means
Slice region Estimate Standard Error DF t Value Pr > |t| Alpha Lower Upper
donorgroup Autoab Pos 1_H 70.5956 1.9683 35 35.87 <.0001 0.05 66.5997 74.5915
donorgroup Autoab Pos 2_B 76.6480 1.9382 35 39.55 <.0001 0.05 72.7132 80.5828
donorgroup Autoab Pos 3_T 78.5377 1.8613 35 42.20 <.0001 0.05 74.7591 82.3164

donorgroup*region Diffs

Simple Differences of donorgroup*region Least Squares Means
Adjustment for Multiple Comparisons: Tukey-Kramer
Slice region region Estimate Standard Error DF t Value Pr > |t| Adj P Alpha Lower Upper Adj Lower Adj Upper
donorgroup Autoab Pos 1_H 2_B -6.0524 2.1908 35 -2.76 0.0091 0.0240 0.05 -10.5000 -1.6048 -11.4139 -0.6909
donorgroup Autoab Pos 1_H 3_T -7.9421 2.0448 35 -3.88 0.0004 0.0012 0.05 -12.0933 -3.7909 -12.9464 -2.9379
donorgroup Autoab Pos 2_B 3_T -1.8897 1.9861 35 -0.95 0.3479 0.6119 0.05 -5.9217 2.1423 -6.7503 2.9708

donorgroup*region LS-Means

Slice of donorgroup*region Least Squares Means
Slice region Estimate Standard Error DF t Value Pr > |t| Alpha Lower Upper
donorgroup Ins. neg. T1D 1_H 72.6299 1.9996 35 36.32 <.0001 0.05 68.5704 76.6893
donorgroup Ins. neg. T1D 2_B 70.8287 2.0720 35 34.18 <.0001 0.05 66.6222 75.0351
donorgroup Ins. neg. T1D 3_T 64.5548 1.9898 35 32.44 <.0001 0.05 60.5153 68.5944

donorgroup*region Diffs

Simple Differences of donorgroup*region Least Squares Means
Adjustment for Multiple Comparisons: Tukey-Kramer
Slice region region Estimate Standard Error DF t Value Pr > |t| Adj P Alpha Lower Upper Adj Lower Adj Upper
donorgroup Ins. neg. T1D 1_H 2_B 1.8012 2.2486 35 0.80 0.4285 0.7049 0.05 -2.7636 6.3660 -3.7016 7.3040
donorgroup Ins. neg. T1D 1_H 3_T 8.0750 2.0855 35 3.87 0.0005 0.0013 0.05 3.8412 12.3088 2.9712 13.1788
donorgroup Ins. neg. T1D 2_B 3_T 6.2738 2.1232 35 2.95 0.0056 0.0150 0.05 1.9635 10.5842 1.0777 11.4700

donorgroup*region LS-Means

Slice of donorgroup*region Least Squares Means
Slice region Estimate Standard Error DF t Value Pr > |t| Alpha Lower Upper
donorgroup Ins. pos. T1D 1_H 71.7618 1.6730 35 42.89 <.0001 0.05 68.3654 75.1582
donorgroup Ins. pos. T1D 2_B 72.8079 1.7336 35 42.00 <.0001 0.05 69.2885 76.3273
donorgroup Ins. pos. T1D 3_T 77.3404 1.6648 35 46.46 <.0001 0.05 73.9606 80.7201

donorgroup*region Diffs

Simple Differences of donorgroup*region Least Squares Means
Adjustment for Multiple Comparisons: Tukey-Kramer
Slice region region Estimate Standard Error DF t Value Pr > |t| Adj P Alpha Lower Upper Adj Lower Adj Upper
donorgroup Ins. pos. T1D 1_H 2_B -1.0461 1.8813 35 -0.56 0.5817 0.8441 0.05 -4.8653 2.7731 -5.6501 3.5579
donorgroup Ins. pos. T1D 1_H 3_T -5.5785 1.7449 35 -3.20 0.0029 0.0081 0.05 -9.1208 -2.0363 -9.8487 -1.3084
donorgroup Ins. pos. T1D 2_B 3_T -4.5325 1.7764 35 -2.55 0.0153 0.0395 0.05 -8.1388 -0.9261 -8.8798 -0.1851

donorgroup*region LS-Means

Slice of donorgroup*region Least Squares Means
Slice region Estimate Standard Error DF t Value Pr > |t| Alpha Lower Upper
donorgroup No diabetes 1_H 73.3827 1.4139 35 51.90 <.0001 0.05 70.5122 76.2532
donorgroup No diabetes 2_B 75.8688 1.5069 35 50.35 <.0001 0.05 72.8097 78.9279
donorgroup No diabetes 3_T 76.6829 1.4070 35 54.50 <.0001 0.05 73.8265 79.5393

donorgroup*region Diffs

Simple Differences of donorgroup*region Least Squares Means
Adjustment for Multiple Comparisons: Tukey-Kramer
Slice region region Estimate Standard Error DF t Value Pr > |t| Adj P Alpha Lower Upper Adj Lower Adj Upper
donorgroup No diabetes 1_H 2_B -2.4861 1.6285 35 -1.53 0.1358 0.2910 0.05 -5.7921 0.8199 -6.4715 1.4992
donorgroup No diabetes 1_H 3_T -3.3002 1.4747 35 -2.24 0.0317 0.0787 0.05 -6.2940 -0.3064 -6.9092 0.3087
donorgroup No diabetes 2_B 3_T -0.8141 1.5421 35 -0.53 0.6009 0.8582 0.05 -3.9447 2.3165 -4.5880 2.9598

Effect Plots

Statement 1

Interaction Plot 1

Interaction Plot for percent_acinar_area by region categorized by donorgroup
In [121]:
%explore(percent_remaining_area);
Out[121]:
SAS Output

SAS Output

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable percent_remaining_area
Covariance Structure Variance Components
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method Parameter
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 1
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 665.66807724  
1 1 665.66807724 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
region nPODCaseI(donorgrou) 28.9555

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 665.7
AIC (Smaller is Better) 667.7
AICC (Smaller is Better) 667.7
BIC (Smaller is Better) 669.3

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
0 0.00 1.0000

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     20.4061 1.4381 35 14.19 <.0001
region   PB 1.7162 2.0726 68 0.83 0.4105
region   PH 4.2103 2.0338 68 2.07 0.0422
region   PT 0 . . . .
donorgroup Autoab Pos   -1.4212 2.3849 35 -0.60 0.5551
donorgroup Ins. neg. T1D   13.6943 2.4909 35 5.50 <.0001
donorgroup Ins. pos. T1D   0.9822 2.2280 35 0.44 0.6620
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB 1.1132 3.3962 68 0.33 0.7441
donorgroup*region Autoab Pos PH 5.1482 3.4485 68 1.49 0.1401
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB -7.4755 3.5452 68 -2.11 0.0387
donorgroup*region Ins. neg. T1D PH -11.3986 3.5227 68 -3.24 0.0019
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 3.3256 3.1760 68 1.05 0.2988
donorgroup*region Ins. pos. T1D PH 1.9457 3.1508 68 0.62 0.5390
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 3.17 0.0485
donorgroup 3 35 9.55 <.0001
donorgroup*region 6 68 3.61 0.0037

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable percent_remaining_area
Covariance Structure Compound Symmetry
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method Profile
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 2
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 665.66807724  
1 2 650.45923843 0.00000002
2 1 650.45923418 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
CS nPODCaseI(donorgrou) 11.6798
Residual   17.2135

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 650.5
AIC (Smaller is Better) 654.5
AICC (Smaller is Better) 654.6
BIC (Smaller is Better) 657.8

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
1 15.21 <.0001

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     20.4061 1.4366 35 14.20 <.0001
region   PB 1.6904 1.6065 68 1.05 0.2964
region   PH 4.2103 1.5681 68 2.68 0.0091
region   PT 0 . . . .
donorgroup Autoab Pos   -1.4212 2.3823 35 -0.60 0.5547
donorgroup Ins. neg. T1D   13.6943 2.4883 35 5.50 <.0001
donorgroup Ins. pos. T1D   0.9822 2.2256 35 0.44 0.6617
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB 1.1390 2.6238 68 0.43 0.6656
donorgroup*region Autoab Pos PH 4.7968 2.6755 68 1.79 0.0774
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB -7.4496 2.7384 68 -2.72 0.0083
donorgroup*region Ins. neg. T1D PH -11.3986 2.7161 68 -4.20 <.0001
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 3.3514 2.4543 68 1.37 0.1766
donorgroup*region Ins. pos. T1D PH 1.9457 2.4294 68 0.80 0.4260
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 4.98 0.0096
donorgroup 3 35 5.38 0.0037
donorgroup*region 6 68 5.88 <.0001

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable percent_remaining_area
Covariance Structure Unstructured
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 6
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 665.66807724  
1 2 650.18975460 0.00000002
2 1 650.18974959 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
UN(1,1) nPODCaseI(donorgrou) 30.1204
UN(2,1) nPODCaseI(donorgrou) 10.9733
UN(2,2) nPODCaseI(donorgrou) 29.2252
UN(3,1) nPODCaseI(donorgrou) 12.1421
UN(3,2) nPODCaseI(donorgrou) 11.8551
UN(3,3) nPODCaseI(donorgrou) 27.3495

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 650.2
AIC (Smaller is Better) 662.2
AICC (Smaller is Better) 663.1
BIC (Smaller is Better) 672.2

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
5 15.48 0.0085

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     20.4061 1.3977 35 14.60 <.0001
region   PB 1.6772 1.5808 35 1.06 0.2960
region   PH 4.2103 1.5321 35 2.75 0.0094
region   PT 0 . . . .
donorgroup Autoab Pos   -1.4212 2.3178 35 -0.61 0.5437
donorgroup Ins. neg. T1D   13.6943 2.4209 35 5.66 <.0001
donorgroup Ins. pos. T1D   0.9822 2.1653 35 0.45 0.6529
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB 1.1522 2.5782 35 0.45 0.6577
donorgroup*region Autoab Pos PH 4.8352 2.6196 35 1.85 0.0734
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB -7.4364 2.6907 35 -2.76 0.0090
donorgroup*region Ins. neg. T1D PH -11.3986 2.6537 35 -4.30 0.0001
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 3.3646 2.4119 35 1.39 0.1718
donorgroup*region Ins. pos. T1D PH 1.9457 2.3736 35 0.82 0.4179
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 35 5.11 0.0113
donorgroup 3 35 5.38 0.0037
donorgroup*region 6 35 6.27 0.0002

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable percent_remaining_area
Covariance Structure Unstructured using Correlations
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 6
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 665.66807724  
1 2 650.18975318 0.00000002
2 1 650.18974959 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 30.1204
Var(2) nPODCaseI(donorgrou) 29.2252
Var(3) nPODCaseI(donorgrou) 27.3495
Corr(2,1) nPODCaseI(donorgrou) 0.3699
Corr(3,1) nPODCaseI(donorgrou) 0.4230
Corr(3,2) nPODCaseI(donorgrou) 0.4193

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 650.2
AIC (Smaller is Better) 662.2
AICC (Smaller is Better) 663.1
BIC (Smaller is Better) 672.2

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
5 15.48 0.0085

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     20.4061 1.3977 35 14.60 <.0001
region   PB 1.6772 1.5808 35 1.06 0.2960
region   PH 4.2103 1.5321 35 2.75 0.0094
region   PT 0 . . . .
donorgroup Autoab Pos   -1.4212 2.3178 35 -0.61 0.5437
donorgroup Ins. neg. T1D   13.6943 2.4209 35 5.66 <.0001
donorgroup Ins. pos. T1D   0.9822 2.1653 35 0.45 0.6529
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB 1.1522 2.5782 35 0.45 0.6577
donorgroup*region Autoab Pos PH 4.8352 2.6196 35 1.85 0.0734
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB -7.4364 2.6907 35 -2.76 0.0090
donorgroup*region Ins. neg. T1D PH -11.3986 2.6537 35 -4.30 0.0001
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 3.3646 2.4119 35 1.39 0.1718
donorgroup*region Ins. pos. T1D PH 1.9457 2.3736 35 0.82 0.4179
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 35 5.11 0.0113
donorgroup 3 35 5.38 0.0037
donorgroup*region 6 35 6.27 0.0002

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable percent_remaining_area
Covariance Structure Banded
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 6
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 45 665.66807724  
1 44 3198.41404873 0.47004321
2 44 3198.41404873 0.47004321

Convergence Status

WARNING: Stopped because of too many likelihood evaluations.

Covariance Parameter Values At Last Iteration

Covariance Parameter Values At Last Iteration
Cov Parm Subject Estimate
UN(1,1) nPODCaseI(donorgrou) 1.0000
UN(2,1) nPODCaseI(donorgrou) 0
UN(2,2) nPODCaseI(donorgrou) 1.0000
UN(3,1) nPODCaseI(donorgrou) 0
UN(3,2) nPODCaseI(donorgrou) 0
UN(3,3) nPODCaseI(donorgrou) 1.0000

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable percent_remaining_area
Covariance Structure Heterogeneous Compound Symmetry
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 4
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 665.66807724  
1 2 650.31787473 0.00000001

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 30.2479
Var(2) nPODCaseI(donorgrou) 29.4163
Var(3) nPODCaseI(donorgrou) 27.0721
CSH nPODCaseI(donorgrou) 0.4049

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 650.3
AIC (Smaller is Better) 658.3
AICC (Smaller is Better) 658.7
BIC (Smaller is Better) 665.0

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
3 15.35 0.0015

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     20.4061 1.3906 35 14.67 <.0001
region   PB 1.6879 1.6020 68 1.05 0.2958
region   PH 4.2103 1.5501 68 2.72 0.0084
region   PT 0 . . . .
donorgroup Autoab Pos   -1.4212 2.3060 35 -0.62 0.5417
donorgroup Ins. neg. T1D   13.6943 2.4086 35 5.69 <.0001
donorgroup Ins. pos. T1D   0.9822 2.1543 35 0.46 0.6512
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB 1.1415 2.6144 68 0.44 0.6638
donorgroup*region Autoab Pos PH 4.7962 2.6476 68 1.81 0.0745
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB -7.4471 2.7285 68 -2.73 0.0081
donorgroup*region Ins. neg. T1D PH -11.3986 2.6848 68 -4.25 <.0001
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 3.3539 2.4457 68 1.37 0.1748
donorgroup*region Ins. pos. T1D PH 1.9457 2.4013 68 0.81 0.4206
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 5.04 0.0091
donorgroup 3 35 5.38 0.0038
donorgroup*region 6 68 6.03 <.0001

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable percent_remaining_area
Covariance Structure Huynh-Feldt
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 4
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 665.66807724  
1 2 650.43493973 0.00000001
2 1 650.43493685 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 29.5605
Var(2) nPODCaseI(donorgrou) 28.8942
Var(3) nPODCaseI(donorgrou) 28.2418
HF nPODCaseI(donorgrou) 17.2156

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 650.4
AIC (Smaller is Better) 658.4
AICC (Smaller is Better) 658.8
BIC (Smaller is Better) 665.1

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
3 15.23 0.0016

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     20.4061 1.4203 35 14.37 <.0001
region   PB 1.6906 1.6072 68 1.05 0.2966
region   PH 4.2103 1.5682 68 2.68 0.0091
region   PT 0 . . . .
donorgroup Autoab Pos   -1.4212 2.3553 35 -0.60 0.5501
donorgroup Ins. neg. T1D   13.6943 2.4600 35 5.57 <.0001
donorgroup Ins. pos. T1D   0.9822 2.2003 35 0.45 0.6581
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB 1.1388 2.6243 68 0.43 0.6657
donorgroup*region Autoab Pos PH 4.7922 2.6757 68 1.79 0.0777
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB -7.4498 2.7390 68 -2.72 0.0083
donorgroup*region Ins. neg. T1D PH -11.3986 2.7163 68 -4.20 <.0001
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 3.3512 2.4548 68 1.37 0.1767
donorgroup*region Ins. pos. T1D PH 1.9457 2.4295 68 0.80 0.4260
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 4.98 0.0096
donorgroup 3 35 5.38 0.0037
donorgroup*region 6 68 5.87 <.0001

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable percent_remaining_area
Covariance Structure Heterogeneous Autoregressive
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 4
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 665.66807724  
1 2 653.90749670 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 30.4800
Var(2) nPODCaseI(donorgrou) 29.3036
Var(3) nPODCaseI(donorgrou) 27.0785
ARH(1) nPODCaseI(donorgrou) 0.3980

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 653.9
AIC (Smaller is Better) 661.9
AICC (Smaller is Better) 662.3
BIC (Smaller is Better) 668.6

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
3 11.76 0.0082

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     20.4061 1.3907 35 14.67 <.0001
region   PB 1.7492 1.8980 68 0.92 0.3600
region   PH 4.2103 1.5575 68 2.70 0.0087
region   PT 0 . . . .
donorgroup Autoab Pos   -1.4212 2.3063 35 -0.62 0.5417
donorgroup Ins. neg. T1D   13.6943 2.4088 35 5.69 <.0001
donorgroup Ins. pos. T1D   0.9822 2.1545 35 0.46 0.6513
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB 1.0802 3.1080 68 0.35 0.7293
donorgroup*region Autoab Pos PH 4.7306 2.6554 68 1.78 0.0793
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB -7.5084 3.2442 68 -2.31 0.0237
donorgroup*region Ins. neg. T1D PH -11.3986 2.6977 68 -4.23 <.0001
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 3.2926 2.9066 68 1.13 0.2613
donorgroup*region Ins. pos. T1D PH 1.9457 2.4129 68 0.81 0.4228
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 5.41 0.0066
donorgroup 3 35 5.92 0.0022
donorgroup*region 6 68 5.70 <.0001

The SAS System

The PRINT Procedure

Data Set WORK.ALL

Description arh1 cs csh hf un unr vc
-2 Res Log Likelihood 653.9 650.5 650.3 650.4 650.2 650.2 665.7
AIC (Smaller is Better) 661.9 654.5 658.3 658.4 662.2 662.2 667.7
AICC (Smaller is Better) 662.3 654.6 658.7 658.8 663.1 663.1 667.7
BIC (Smaller is Better) 668.6 657.8 665.0 665.1 672.2 672.2 669.3

The SAS System

The PRINT Procedure

Data Set WORK.STATUS

Obs Reason Status pdG pdH covar
1 Convergence criteria met. 0 1 1 arh(1)
2 Convergence criteria met. 0 1 1 cs
3 Convergence criteria met. 0 1 1 csh
4 Convergence criteria met. 0 1 1 hf
5 Convergence criteria met. 0 1 1 un
6 WARNING: Stopped because of too many likelihood evaluations. 1 1 1 un1
7 Convergence criteria met. 0 1 1 unr
8 Convergence criteria met. 0 1 1 vc
In [122]:
PROC mixed data=cell3 /*maxiter=1000 maxfunc=5000  can also use covtest*/;
format region $regionformat.;
     class nPODCaseID donorgroup region;
     model  percent_remaining_area =region|donorgroup/solution; /*can use  ddfm = kenwardroger after solution for unbalanced data to improve performance of t and f tests*/
     /*option e3 after solution helps to describe how type 3 tests were constructed*/
     repeated  region/ subject=nPODCaseID(donorgroup)  type=un; 
     lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;
       store remaining_model_data;
run;

proc plm restore=remaining_model_data;
effectplot interaction(sliceby=donorgroup);
slice donorgroup*region/sliceby=donorgroup diff adjust=tukey cl pdiff alpha=0.05 plots=none nof means;
run;
Out[122]:
SAS Output

SAS Output

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable percent_remaining_area
Covariance Structure Unstructured
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 1_H 2_B 3_T

Dimensions

Dimensions
Covariance Parameters 6
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 665.66807724  
1 2 650.18975460 0.00000002
2 1 650.18974959 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
UN(1,1) nPODCaseI(donorgrou) 29.2252
UN(2,1) nPODCaseI(donorgrou) 10.9733
UN(2,2) nPODCaseI(donorgrou) 30.1204
UN(3,1) nPODCaseI(donorgrou) 11.8551
UN(3,2) nPODCaseI(donorgrou) 12.1421
UN(3,3) nPODCaseI(donorgrou) 27.3495

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 650.2
AIC (Smaller is Better) 662.2
AICC (Smaller is Better) 663.1
BIC (Smaller is Better) 672.2

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
5 15.48 0.0085

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     20.4061 1.3977 35 14.60 <.0001
region   1_H 4.2103 1.5321 35 2.75 0.0094
region   2_B 1.6772 1.5808 35 1.06 0.2960
region   3_T 0 . . . .
donorgroup Autoab Pos   -1.4212 2.3178 35 -0.61 0.5437
donorgroup Ins. neg. T1D   13.6943 2.4209 35 5.66 <.0001
donorgroup Ins. pos. T1D   0.9822 2.1653 35 0.45 0.6529
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos 1_H 4.8352 2.6196 35 1.85 0.0734
donorgroup*region Autoab Pos 2_B 1.1522 2.5782 35 0.45 0.6577
donorgroup*region Autoab Pos 3_T 0 . . . .
donorgroup*region Ins. neg. T1D 1_H -11.3986 2.6537 35 -4.30 0.0001
donorgroup*region Ins. neg. T1D 2_B -7.4364 2.6907 35 -2.76 0.0090
donorgroup*region Ins. neg. T1D 3_T 0 . . . .
donorgroup*region Ins. pos. T1D 1_H 1.9457 2.3736 35 0.82 0.4179
donorgroup*region Ins. pos. T1D 2_B 3.3646 2.4119 35 1.39 0.1718
donorgroup*region Ins. pos. T1D 3_T 0 . . . .
donorgroup*region No diabetes 1_H 0 . . . .
donorgroup*region No diabetes 2_B 0 . . . .
donorgroup*region No diabetes 3_T 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 35 5.11 0.0113
donorgroup 3 35 5.38 0.0037
donorgroup*region 6 35 6.27 0.0002

Least Squares Means

Least Squares Means
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t| Alpha Lower Upper
region   1_H 26.7758 0.9098 35 29.43 <.0001 0.05 24.9288 28.6229
region   2_B 24.6673 0.9138 35 26.99 <.0001 0.05 22.8122 26.5223
region   3_T 23.7200 0.8665 35 27.37 <.0001 0.05 21.9608 25.4791
donorgroup Autoab Pos   22.9433 1.4902 35 15.40 <.0001 0.05 19.9180 25.9685
donorgroup Ins. neg. T1D   29.7846 1.5768 35 18.89 <.0001 0.05 26.5835 32.9857
donorgroup Ins. pos. T1D   25.1210 1.3192 35 19.04 <.0001 0.05 22.4428 27.7992
donorgroup No diabetes   22.3686 1.1213 35 19.95 <.0001 0.05 20.0922 24.6451
donorgroup*region Autoab Pos 1_H 28.0305 2.0149 35 13.91 <.0001 0.05 23.9401 32.1209
donorgroup*region Autoab Pos 2_B 21.8144 1.9404 35 11.24 <.0001 0.05 17.8752 25.7535
donorgroup*region Autoab Pos 3_T 18.9849 1.8490 35 10.27 <.0001 0.05 15.2313 22.7386
donorgroup*region Ins. neg. T1D 1_H 26.9121 2.0433 35 13.17 <.0001 0.05 22.7640 31.0602
donorgroup*region Ins. neg. T1D 2_B 28.3412 2.0743 35 13.66 <.0001 0.05 24.1301 32.5524
donorgroup*region Ins. neg. T1D 3_T 34.1004 1.9766 35 17.25 <.0001 0.05 30.0876 38.1132
donorgroup*region Ins. pos. T1D 1_H 27.5444 1.7095 35 16.11 <.0001 0.05 24.0738 31.0149
donorgroup*region Ins. pos. T1D 2_B 26.4302 1.7355 35 15.23 <.0001 0.05 22.9069 29.9535
donorgroup*region Ins. pos. T1D 3_T 21.3883 1.6538 35 12.93 <.0001 0.05 18.0310 24.7457
donorgroup*region No diabetes 1_H 24.6164 1.4448 35 17.04 <.0001 0.05 21.6833 27.5496
donorgroup*region No diabetes 2_B 22.0833 1.5099 35 14.63 <.0001 0.05 19.0180 25.1486
donorgroup*region No diabetes 3_T 20.4061 1.3977 35 14.60 <.0001 0.05 17.5687 23.2436

Differences of Least Squares Means

Differences of Least Squares Means
Effect donorgroup region _donorgroup region Estimate Standard
Error
DF t Value Pr > |t| Adjustment Adj P Alpha Lower Upper Adj Lower Adj Upper
region   1_H   2_B 2.1086 1.0297 35 2.05 0.0481 Tukey-Kramer 0.1158 0.05 0.01822 4.1989 -0.4113 4.6285
region   1_H   3_T 3.0559 0.9632 35 3.17 0.0031 Tukey-Kramer 0.0086 0.05 1.1005 5.0113 0.6987 5.4131
region   2_B   3_T 0.9473 0.9587 35 0.99 0.3299 Tukey-Kramer 0.5891 0.05 -0.9990 2.8936 -1.3990 3.2936
donorgroup Autoab Pos   Ins. neg. T1D   -6.8413 2.1696 35 -3.15 0.0033 Tukey-Kramer 0.0166 0.05 -11.2458 -2.4369 -12.6924 -0.9903
donorgroup Autoab Pos   Ins. pos. T1D   -2.1777 1.9902 35 -1.09 0.2813 Tukey-Kramer 0.6954 0.05 -6.2181 1.8627 -7.5452 3.1898
donorgroup Autoab Pos   No diabetes   0.5746 1.8650 35 0.31 0.7598 Tukey-Kramer 0.9897 0.05 -3.2114 4.3607 -4.4550 5.6043
donorgroup Ins. neg. T1D   Ins. pos. T1D   4.6636 2.0559 35 2.27 0.0296 Tukey-Kramer 0.1252 0.05 0.4899 8.8373 -0.8809 10.2082
donorgroup Ins. neg. T1D   No diabetes   7.4160 1.9349 35 3.83 0.0005 Tukey-Kramer 0.0027 0.05 3.4880 11.3440 2.1978 12.6341
donorgroup Ins. pos. T1D   No diabetes   2.7523 1.7314 35 1.59 0.1209 Tukey-Kramer 0.3975 0.05 -0.7626 6.2673 -1.9171 7.4218
donorgroup*region Autoab Pos 1_H Autoab Pos 2_B 6.2161 2.2542 35 2.76 0.0092 Tukey-Kramer 0.2416 0.05 1.6398 10.7924 -1.6665 14.0987
donorgroup*region Autoab Pos 1_H Autoab Pos 3_T 9.0455 2.1248 35 4.26 0.0001 Tukey-Kramer 0.0070 0.05 4.7320 13.3590 1.6156 16.4755
donorgroup*region Autoab Pos 1_H Ins. neg. T1D 1_H 1.1183 2.8696 35 0.39 0.6991 Tukey-Kramer 1.0000 0.05 -4.7073 6.9440 -8.9163 11.1529
donorgroup*region Autoab Pos 1_H Ins. neg. T1D 2_B -0.3107 2.8918 35 -0.11 0.9150 Tukey-Kramer 1.0000 0.05 -6.1814 5.5600 -10.4230 9.8015
donorgroup*region Autoab Pos 1_H Ins. neg. T1D 3_T -6.0699 2.8225 35 -2.15 0.0385 Tukey-Kramer 0.5928 0.05 -11.8000 -0.3399 -15.9399 3.8000
donorgroup*region Autoab Pos 1_H Ins. pos. T1D 1_H 0.4861 2.6424 35 0.18 0.8551 Tukey-Kramer 1.0000 0.05 -4.8782 5.8505 -8.7539 9.7261
donorgroup*region Autoab Pos 1_H Ins. pos. T1D 2_B 1.6003 2.6593 35 0.60 0.5512 Tukey-Kramer 1.0000 0.05 -3.7983 6.9989 -7.6988 10.8993
donorgroup*region Autoab Pos 1_H Ins. pos. T1D 3_T 6.6421 2.6067 35 2.55 0.0154 Tukey-Kramer 0.3455 0.05 1.3503 11.9339 -2.4729 15.7572
donorgroup*region Autoab Pos 1_H No diabetes 1_H 3.4140 2.4794 35 1.38 0.1773 Tukey-Kramer 0.9605 0.05 -1.6193 8.4474 -5.2559 12.0840
donorgroup*region Autoab Pos 1_H No diabetes 2_B 5.9472 2.5179 35 2.36 0.0239 Tukey-Kramer 0.4556 0.05 0.8356 11.0587 -2.8574 14.7517
donorgroup*region Autoab Pos 1_H No diabetes 3_T 7.6244 2.4522 35 3.11 0.0037 Tukey-Kramer 0.1205 0.05 2.6461 12.6026 -0.9506 16.1993
donorgroup*region Autoab Pos 2_B Autoab Pos 3_T 2.8294 2.0367 35 1.39 0.1735 Tukey-Kramer 0.9581 0.05 -1.3053 6.9642 -4.2926 9.9515
donorgroup*region Autoab Pos 2_B Ins. neg. T1D 1_H -5.0978 2.8178 35 -1.81 0.0790 Tukey-Kramer 0.8023 0.05 -10.8182 0.6227 -14.9512 4.7557
donorgroup*region Autoab Pos 2_B Ins. neg. T1D 2_B -6.5268 2.8404 35 -2.30 0.0277 Tukey-Kramer 0.4964 0.05 -12.2932 -0.7605 -16.4593 3.4056
donorgroup*region Autoab Pos 2_B Ins. neg. T1D 3_T -12.2861 2.7699 35 -4.44 <.0001 Tukey-Kramer 0.0043 0.05 -17.9092 -6.6629 -21.9718 -2.6003
donorgroup*region Autoab Pos 2_B Ins. pos. T1D 1_H -5.7300 2.5860 35 -2.22 0.0333 Tukey-Kramer 0.5499 0.05 -10.9799 -0.4801 -14.7729 3.3129
donorgroup*region Autoab Pos 2_B Ins. pos. T1D 2_B -4.6158 2.6033 35 -1.77 0.0849 Tukey-Kramer 0.8211 0.05 -9.9008 0.6691 -13.7191 4.4874
donorgroup*region Autoab Pos 2_B Ins. pos. T1D 3_T 0.4260 2.5495 35 0.17 0.8683 Tukey-Kramer 1.0000 0.05 -4.7498 5.6018 -8.4892 9.3412
donorgroup*region Autoab Pos 2_B No diabetes 1_H -2.8021 2.4192 35 -1.16 0.2546 Tukey-Kramer 0.9890 0.05 -7.7133 2.1092 -11.2616 5.6575
donorgroup*region Autoab Pos 2_B No diabetes 2_B -0.2689 2.4586 35 -0.11 0.9135 Tukey-Kramer 1.0000 0.05 -5.2603 4.7224 -8.8664 8.3285
donorgroup*region Autoab Pos 2_B No diabetes 3_T 1.4083 2.3914 35 0.59 0.5597 Tukey-Kramer 1.0000 0.05 -3.4465 6.2630 -6.9539 9.7704
donorgroup*region Autoab Pos 3_T Ins. neg. T1D 1_H -7.9272 2.7557 35 -2.88 0.0068 Tukey-Kramer 0.1933 0.05 -13.5215 -2.3329 -17.5633 1.7089
donorgroup*region Autoab Pos 3_T Ins. neg. T1D 2_B -9.3563 2.7788 35 -3.37 0.0019 Tukey-Kramer 0.0679 0.05 -14.9975 -3.7150 -19.0732 0.3607
donorgroup*region Autoab Pos 3_T Ins. neg. T1D 3_T -15.1155 2.7066 35 -5.58 <.0001 Tukey-Kramer 0.0002 0.05 -20.6102 -9.6207 -24.5800 -5.6509
donorgroup*region Autoab Pos 3_T Ins. pos. T1D 1_H -8.5594 2.5182 35 -3.40 0.0017 Tukey-Kramer 0.0630 0.05 -13.6716 -3.4472 -17.3650 0.2462
donorgroup*region Autoab Pos 3_T Ins. pos. T1D 2_B -7.4452 2.5359 35 -2.94 0.0058 Tukey-Kramer 0.1721 0.05 -12.5934 -2.2971 -16.3128 1.4223
donorgroup*region Autoab Pos 3_T Ins. pos. T1D 3_T -2.4034 2.4807 35 -0.97 0.3393 Tukey-Kramer 0.9975 0.05 -7.4394 2.6326 -11.0778 6.2710
donorgroup*region Autoab Pos 3_T No diabetes 1_H -5.6315 2.3465 35 -2.40 0.0219 Tukey-Kramer 0.4321 0.05 -10.3952 -0.8678 -13.8369 2.5739
donorgroup*region Autoab Pos 3_T No diabetes 2_B -3.0984 2.3872 35 -1.30 0.2028 Tukey-Kramer 0.9740 0.05 -7.9446 1.7479 -11.4459 5.2492
donorgroup*region Autoab Pos 3_T No diabetes 3_T -1.4212 2.3178 35 -0.61 0.5437 Tukey-Kramer 1.0000 0.05 -6.1266 3.2842 -9.5261 6.6838
donorgroup*region Ins. neg. T1D 1_H Ins. neg. T1D 2_B -1.4291 2.3114 35 -0.62 0.5404 Tukey-Kramer 1.0000 0.05 -6.1215 3.2634 -9.5118 6.6536
donorgroup*region Ins. neg. T1D 1_H Ins. neg. T1D 3_T -7.1883 2.1668 35 -3.32 0.0021 Tukey-Kramer 0.0761 0.05 -11.5871 -2.7895 -14.7651 0.3886
donorgroup*region Ins. neg. T1D 1_H Ins. pos. T1D 1_H -0.6322 2.6641 35 -0.24 0.8138 Tukey-Kramer 1.0000 0.05 -6.0407 4.7762 -9.9482 8.6838
donorgroup*region Ins. neg. T1D 1_H Ins. pos. T1D 2_B 0.4819 2.6809 35 0.18 0.8584 Tukey-Kramer 1.0000 0.05 -4.9605 5.9244 -8.8926 9.8565
donorgroup*region Ins. neg. T1D 1_H Ins. pos. T1D 3_T 5.5238 2.6287 35 2.10 0.0429 Tukey-Kramer 0.6251 0.05 0.1873 10.8603 -3.6683 14.7159
donorgroup*region Ins. neg. T1D 1_H No diabetes 1_H 2.2957 2.5025 35 0.92 0.3652 Tukey-Kramer 0.9984 0.05 -2.7846 7.3761 -6.4551 11.0466
donorgroup*region Ins. neg. T1D 1_H No diabetes 2_B 4.8288 2.5407 35 1.90 0.0656 Tukey-Kramer 0.7510 0.05 -0.3290 9.9866 -4.0554 13.7131
donorgroup*region Ins. neg. T1D 1_H No diabetes 3_T 6.5060 2.4756 35 2.63 0.0127 Tukey-Kramer 0.3031 0.05 1.4803 11.5317 -2.1507 15.1628
donorgroup*region Ins. neg. T1D 2_B Ins. neg. T1D 3_T -5.7592 2.1773 35 -2.65 0.0121 Tukey-Kramer 0.2945 0.05 -10.1795 -1.3390 -13.3730 1.8546
donorgroup*region Ins. neg. T1D 2_B Ins. pos. T1D 1_H 0.7969 2.6880 35 0.30 0.7686 Tukey-Kramer 1.0000 0.05 -4.6601 6.2538 -8.6027 10.1964
donorgroup*region Ins. neg. T1D 2_B Ins. pos. T1D 2_B 1.9110 2.7046 35 0.71 0.4845 Tukey-Kramer 0.9999 0.05 -3.5797 7.4017 -7.5466 11.3686
donorgroup*region Ins. neg. T1D 2_B Ins. pos. T1D 3_T 6.9529 2.6529 35 2.62 0.0129 Tukey-Kramer 0.3067 0.05 1.5672 12.3385 -2.3239 16.2296
donorgroup*region Ins. neg. T1D 2_B No diabetes 1_H 3.7248 2.5279 35 1.47 0.1496 Tukey-Kramer 0.9382 0.05 -1.4072 8.8567 -5.1150 12.5645
donorgroup*region Ins. neg. T1D 2_B No diabetes 2_B 6.2579 2.5657 35 2.44 0.0199 Tukey-Kramer 0.4083 0.05 1.0492 11.4665 -2.7139 15.2297
donorgroup*region Ins. neg. T1D 2_B No diabetes 3_T 7.9351 2.5013 35 3.17 0.0031 Tukey-Kramer 0.1052 0.05 2.8572 13.0130 -0.8115 16.6817
donorgroup*region Ins. neg. T1D 3_T Ins. pos. T1D 1_H 6.5561 2.6133 35 2.51 0.0169 Tukey-Kramer 0.3676 0.05 1.2507 11.8614 -2.5824 15.6945
donorgroup*region Ins. neg. T1D 3_T Ins. pos. T1D 2_B 7.6702 2.6304 35 2.92 0.0062 Tukey-Kramer 0.1791 0.05 2.3302 13.0103 -1.5279 16.8684
donorgroup*region Ins. neg. T1D 3_T Ins. pos. T1D 3_T 12.7121 2.5772 35 4.93 <.0001 Tukey-Kramer 0.0010 0.05 7.4801 17.9441 3.7000 21.7241
donorgroup*region Ins. neg. T1D 3_T No diabetes 1_H 9.4840 2.4484 35 3.87 0.0004 Tukey-Kramer 0.0195 0.05 4.5135 14.4545 0.9224 18.0456
donorgroup*region Ins. neg. T1D 3_T No diabetes 2_B 12.0171 2.4874 35 4.83 <.0001 Tukey-Kramer 0.0014 0.05 6.9675 17.0667 3.3192 20.7150
donorgroup*region Ins. neg. T1D 3_T No diabetes 3_T 13.6943 2.4209 35 5.66 <.0001 Tukey-Kramer 0.0001 0.05 8.7797 18.6089 5.2289 22.1597
donorgroup*region Ins. pos. T1D 1_H Ins. pos. T1D 2_B 1.1142 1.9339 35 0.58 0.5682 Tukey-Kramer 1.0000 0.05 -2.8118 5.0402 -5.6483 7.8766
donorgroup*region Ins. pos. T1D 1_H Ins. pos. T1D 3_T 6.1560 1.8129 35 3.40 0.0017 Tukey-Kramer 0.0635 0.05 2.4757 9.8363 -0.1832 12.4953
donorgroup*region Ins. pos. T1D 1_H No diabetes 1_H 2.9279 2.2383 35 1.31 0.1994 Tukey-Kramer 0.9725 0.05 -1.6161 7.4719 -4.8991 10.7549
donorgroup*region Ins. pos. T1D 1_H No diabetes 2_B 5.4610 2.2809 35 2.39 0.0221 Tukey-Kramer 0.4356 0.05 0.8306 10.0915 -2.5148 13.4369
donorgroup*region Ins. pos. T1D 1_H No diabetes 3_T 7.1382 2.2082 35 3.23 0.0027 Tukey-Kramer 0.0921 0.05 2.6554 11.6211 -0.5834 14.8599
donorgroup*region Ins. pos. T1D 2_B Ins. pos. T1D 3_T 5.0418 1.8217 35 2.77 0.0090 Tukey-Kramer 0.2372 0.05 1.3436 8.7401 -1.3283 11.4120
donorgroup*region Ins. pos. T1D 2_B No diabetes 1_H 1.8138 2.2582 35 0.80 0.4273 Tukey-Kramer 0.9995 0.05 -2.7707 6.3982 -6.0829 9.7104
donorgroup*region Ins. pos. T1D 2_B No diabetes 2_B 4.3469 2.3004 35 1.89 0.0671 Tukey-Kramer 0.7574 0.05 -0.3232 9.0170 -3.6973 12.3911
donorgroup*region Ins. pos. T1D 2_B No diabetes 3_T 6.0241 2.2284 35 2.70 0.0105 Tukey-Kramer 0.2662 0.05 1.5003 10.5479 -1.7681 13.8163
donorgroup*region Ins. pos. T1D 3_T No diabetes 1_H -3.2281 2.1960 35 -1.47 0.1505 Tukey-Kramer 0.9391 0.05 -7.6862 1.2301 -10.9072 4.4510
donorgroup*region Ins. pos. T1D 3_T No diabetes 2_B -0.6950 2.2394 35 -0.31 0.7581 Tukey-Kramer 1.0000 0.05 -5.2412 3.8512 -8.5257 7.1358
donorgroup*region Ins. pos. T1D 3_T No diabetes 3_T 0.9822 2.1653 35 0.45 0.6529 Tukey-Kramer 1.0000 0.05 -3.4135 5.3780 -6.5894 8.5539
donorgroup*region No diabetes 1_H No diabetes 2_B 2.5331 1.6733 35 1.51 0.1390 Tukey-Kramer 0.9266 0.05 -0.8638 5.9300 -3.3180 8.3842
donorgroup*region No diabetes 1_H No diabetes 3_T 4.2103 1.5321 35 2.75 0.0094 Tukey-Kramer 0.2458 0.05 1.0999 7.3207 -1.1473 9.5680
donorgroup*region No diabetes 2_B No diabetes 3_T 1.6772 1.5808 35 1.06 0.2960 Tukey-Kramer 0.9946 0.05 -1.5320 4.8863 -3.8505 7.2049

The SAS System

The PLM Procedure

The PLM Procedure

Store Information

Store Information
Item Store WORK.REMAINING_MODEL_DATA
Data Set Created From WORK.CELL3
Created By PROC MIXED
Date Created 12NOV20:01:21:15
Response Variable percent_remaining_area
Distribution Normal
Class Variables nPODCaseID donorgroup region
Model Effects Intercept region donorgroup donorgroup*region

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 1_H 2_B 3_T

Slices

donorgroup*region LS-Means

Slice of donorgroup*region Least Squares Means
Slice region Estimate Standard Error DF t Value Pr > |t| Alpha Lower Upper
donorgroup Autoab Pos 1_H 28.0305 2.0149 35 13.91 <.0001 0.05 23.9401 32.1209
donorgroup Autoab Pos 2_B 21.8144 1.9404 35 11.24 <.0001 0.05 17.8752 25.7535
donorgroup Autoab Pos 3_T 18.9849 1.8490 35 10.27 <.0001 0.05 15.2313 22.7386

donorgroup*region Diffs

Simple Differences of donorgroup*region Least Squares Means
Adjustment for Multiple Comparisons: Tukey-Kramer
Slice region region Estimate Standard Error DF t Value Pr > |t| Adj P Alpha Lower Upper Adj Lower Adj Upper
donorgroup Autoab Pos 1_H 2_B 6.2161 2.2542 35 2.76 0.0092 0.0243 0.05 1.6398 10.7924 0.6994 11.7328
donorgroup Autoab Pos 1_H 3_T 9.0455 2.1248 35 4.26 0.0001 0.0004 0.05 4.7320 13.3590 3.8456 14.2454
donorgroup Autoab Pos 2_B 3_T 2.8294 2.0367 35 1.39 0.1735 0.3574 0.05 -1.3053 6.9642 -2.1550 7.8138

donorgroup*region LS-Means

Slice of donorgroup*region Least Squares Means
Slice region Estimate Standard Error DF t Value Pr > |t| Alpha Lower Upper
donorgroup Ins. neg. T1D 1_H 26.9121 2.0433 35 13.17 <.0001 0.05 22.7640 31.0602
donorgroup Ins. neg. T1D 2_B 28.3412 2.0743 35 13.66 <.0001 0.05 24.1301 32.5524
donorgroup Ins. neg. T1D 3_T 34.1004 1.9766 35 17.25 <.0001 0.05 30.0876 38.1132

donorgroup*region Diffs

Simple Differences of donorgroup*region Least Squares Means
Adjustment for Multiple Comparisons: Tukey-Kramer
Slice region region Estimate Standard Error DF t Value Pr > |t| Adj P Alpha Lower Upper Adj Lower Adj Upper
donorgroup Ins. neg. T1D 1_H 2_B -1.4291 2.3114 35 -0.62 0.5404 0.8111 0.05 -6.1215 3.2634 -7.0858 4.2276
donorgroup Ins. neg. T1D 1_H 3_T -7.1883 2.1668 35 -3.32 0.0021 0.0059 0.05 -11.5871 -2.7895 -12.4910 -1.8856
donorgroup Ins. neg. T1D 2_B 3_T -5.7592 2.1773 35 -2.65 0.0121 0.0318 0.05 -10.1795 -1.3390 -11.0878 -0.4307

donorgroup*region LS-Means

Slice of donorgroup*region Least Squares Means
Slice region Estimate Standard Error DF t Value Pr > |t| Alpha Lower Upper
donorgroup Ins. pos. T1D 1_H 27.5444 1.7095 35 16.11 <.0001 0.05 24.0738 31.0149
donorgroup Ins. pos. T1D 2_B 26.4302 1.7355 35 15.23 <.0001 0.05 22.9069 29.9535
donorgroup Ins. pos. T1D 3_T 21.3883 1.6538 35 12.93 <.0001 0.05 18.0310 24.7457

donorgroup*region Diffs

Simple Differences of donorgroup*region Least Squares Means
Adjustment for Multiple Comparisons: Tukey-Kramer
Slice region region Estimate Standard Error DF t Value Pr > |t| Adj P Alpha Lower Upper Adj Lower Adj Upper
donorgroup Ins. pos. T1D 1_H 2_B 1.1142 1.9339 35 0.58 0.5682 0.8337 0.05 -2.8118 5.0402 -3.6186 5.8469
donorgroup Ins. pos. T1D 1_H 3_T 6.1560 1.8129 35 3.40 0.0017 0.0048 0.05 2.4757 9.8363 1.7195 10.5926
donorgroup Ins. pos. T1D 2_B 3_T 5.0418 1.8217 35 2.77 0.0090 0.0238 0.05 1.3436 8.7401 0.5837 9.5000

donorgroup*region LS-Means

Slice of donorgroup*region Least Squares Means
Slice region Estimate Standard Error DF t Value Pr > |t| Alpha Lower Upper
donorgroup No diabetes 1_H 24.6164 1.4448 35 17.04 <.0001 0.05 21.6833 27.5496
donorgroup No diabetes 2_B 22.0833 1.5099 35 14.63 <.0001 0.05 19.0180 25.1486
donorgroup No diabetes 3_T 20.4061 1.3977 35 14.60 <.0001 0.05 17.5687 23.2436

donorgroup*region Diffs

Simple Differences of donorgroup*region Least Squares Means
Adjustment for Multiple Comparisons: Tukey-Kramer
Slice region region Estimate Standard Error DF t Value Pr > |t| Adj P Alpha Lower Upper Adj Lower Adj Upper
donorgroup No diabetes 1_H 2_B 2.5331 1.6733 35 1.51 0.1390 0.2968 0.05 -0.8638 5.9300 -1.5618 6.6280
donorgroup No diabetes 1_H 3_T 4.2103 1.5321 35 2.75 0.0094 0.0249 0.05 1.0999 7.3207 0.4608 7.9599
donorgroup No diabetes 2_B 3_T 1.6772 1.5808 35 1.06 0.2960 0.5442 0.05 -1.5320 4.8863 -2.1914 5.5458

Effect Plots

Statement 1

Interaction Plot 1

Interaction Plot for percent_remaining_area by region categorized by donorgroup

Figure 3b

for figure 3b: evaluate weight in all three tissue types. formula for mass (g per pancreas) is the ratio of tissue area (sub-tissue area/whole pancreas tissue areas) times whole pancreas weight

In [123]:
DATA allclinical;
    set clinical1;
    if pancreas_received_intact="FALSE" then delete;
    if whole_pancreas_g=. then delete;
    if oppc_weightR=. then delete;
    weight_g=oppc_weightR*1000;

    
    /*bring in finding from study regarding insulin positivity (main data)*/
    insulin_positive="INS+";
    if npodcaseid=6062 then insulin_positive="INS-";
    if npodcaseid=6079 then insulin_positive="INS-";
    if npodcaseid=6087 then insulin_positive="INS-";
    if npodcaseid=6360 then insulin_positive="INS-";
    if npodcaseid=6064 then insulin_positive="INS-";
    if npodcaseid=6089 then insulin_positive="INS-";
    if npodcaseid=6237 then insulin_positive="INS-";
RUN;

PROC sort data=allclinical;
    by npodcaseID;
RUN;

DATA area (keep= npodcaseID mean_percent_endocrine_area mean_percent_acinar_area mean_percent_remaining_area);
    set cell3_combined_donorgroup;
RUN;


PROC sort data=area out=area1 noduprecs;
    by _all_;
RUN;


DATA weight;
    merge allclinical(in=a) area1 (in=b);
    by npodcaseID;
    if b;
RUN;

/* 
to calculate sub-tissue as percentage of pancreas weight:     endocrine_weight=((mean_percent_endocrine_area/100)*(whole_pancreas_g))/whole_pancreas_g*100;
to calculate sub-tissue as percentage of whole body weight: endocrine_weight=((mean_percent_endocrine_area/100)*(whole_pancreas_g))/weight_g*100;

*/

DATA weight1;
    set weight;
    endocrine_weight=((mean_percent_endocrine_area/100)*(whole_pancreas_g))/weight_g*100; 
    acinar_weight=((mean_percent_acinar_area/100)*(whole_pancreas_g))/weight_g*100;
    remaining_weight=((mean_percent_remaining_area/100)*(whole_pancreas_g))/weight_g*100;
    total_weight=endocrine_weight + acinar_weight + remaining_weight;
    donor_group_specific="          ";
    if donortype="No diabetes" then donor_group_specific="ND";
    if donortype="Autoab Pos" then donor_group_specific="AAb+";
    if donortype="T1D" and insulin_positive="INS+" then donor_group_specific="T1D INS+";
    if donortype="T1D" and insulin_positive="INS-" then donor_group_specific="T1D INS-";
    
    endocrine_weight1=((mean_percent_endocrine_area/100)*(whole_pancreas_g));
    acinar_weight1=((mean_percent_acinar_area/100)*(whole_pancreas_g));
    remaining_weight1=((mean_percent_remaining_area/100)*(whole_pancreas_g));
    total_weight1=endocrine_weight1 + acinar_weight1 + remaining_weight1;
    
    
    
RUN;


PROC sort data=weight1;
by donor_group_specific;
run;


PROC means data=weight1 n mean std median min max;
by donor_group_specific;
var endocrine_weight acinar_weight remaining_weight total_weight relative;
run;

proc export data=weight1
     outfile="&location\Data\weight_wide.csv" 
     dbms=csv
     replace;
run;


/*prep for graphing in R*/
PROC sort data=weight1;
by nPODCaseID donor_group_specific;
run;

PROC transpose data=weight1 out=weight2;
    by nPODCaseID donor_group_specific;
    var endocrine_weight acinar_weight remaining_weight;
RUN;

DATA weight2;
    set weight2;
    rename _NAME_=tissue;
    if col1=. then delete;
RUN;

proc export data=weight2
     outfile="&location\Data\weight_long.csv" 
     dbms=csv
     replace;
run;
Out[123]:
SAS Output

SAS Output

The SAS System

The MEANS Procedure

The MEANS Procedure

donor_group_specific=' '

Summary statistics

Variable N Mean Std Dev Median Minimum Maximum
endocrine_weight
acinar_weight
remaining_weight
total_weight
relative
0
0
0
0
0
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

donor_group_specific=AAb+

Summary statistics

Variable N Mean Std Dev Median Minimum Maximum
endocrine_weight
acinar_weight
remaining_weight
total_weight
relative
7
7
7
7
7
0.0016216
0.0712000
0.0215784
0.0944000
0.0944000
0.000733043
0.0215887
0.0044120
0.0246025
0.0246025
0.0015244
0.0585649
0.0221235
0.0823596
0.0823596
0.000947131
0.0484705
0.0136149
0.0631080
0.0631080
0.0030060
0.1033716
0.0255476
0.1274118
0.1274118

donor_group_specific=ND

Summary statistics

Variable N Mean Std Dev Median Minimum Maximum
endocrine_weight
acinar_weight
remaining_weight
total_weight
relative
12
12
12
12
12
0.0021102
0.0683091
0.0209770
0.0913962
0.0913962
0.000520035
0.0240860
0.0065730
0.0305142
0.0305142
0.0021629
0.0646022
0.0215698
0.0886681
0.0886681
0.0013371
0.0393608
0.0092945
0.0531867
0.0531867
0.0031328
0.1251003
0.0334150
0.1607333
0.1607333

donor_group_specific=T1D INS+

Summary statistics

Variable N Mean Std Dev Median Minimum Maximum
endocrine_weight
acinar_weight
remaining_weight
total_weight
relative
8
8
8
8
8
0.000487288
0.0484723
0.0166774
0.0656370
0.0656370
0.000255354
0.0170051
0.0049181
0.0213731
0.0213731
0.000424681
0.0470388
0.0157524
0.0610135
0.0610135
0.000153896
0.0278126
0.0115918
0.0397333
0.0397333
0.000963674
0.0837213
0.0271273
0.1112338
0.1112338

donor_group_specific=T1D INS-

Summary statistics

Variable N Mean Std Dev Median Minimum Maximum
endocrine_weight
acinar_weight
remaining_weight
total_weight
relative
7
7
7
7
7
0.000527998
0.0448263
0.0181333
0.0634877
0.0634877
0.000111124
0.0168432
0.0038072
0.0201684
0.0201684
0.000535751
0.0478578
0.0197367
0.0689535
0.0689535
0.000394468
0.0234263
0.0127862
0.0379167
0.0379167
0.000718708
0.0642346
0.0230778
0.0845070
0.0845070

look at association between c-peptide and various weights

In [124]:
proc corr data=weight1; 
var oppc_c_peptideR1 endocrine_weight1 acinar_weight1 remaining_weight1 total_weight1 mean_percent_endocrine_area mean_percent_acinar_area mean_percent_remaining_area;
run;
Out[124]:
SAS Output

SAS Output

The SAS System

The CORR Procedure

The CORR Procedure

Variables Information

8 Variables: oppc_c_peptideR1 endocrine_weight1 acinar_weight1 remaining_weight1 total_weight1 mean_percent_endocrine_area mean_percent_acinar_area mean_percent_remaining_area

Simple Statistics

Simple Statistics
Variable N Mean Std Dev Sum Minimum Maximum
oppc_c_peptideR1 33 3.68909 5.06408 121.74000 0.02000 17.48000
endocrine_weight1 34 0.68982 0.50887 23.45378 0.06156 1.82528
acinar_weight1 34 32.18888 16.96750 1094 7.40537 85.30814
remaining_weight1 34 10.64659 5.01324 361.98420 2.80018 23.96221
total_weight1 34 43.52529 21.96830 1480 10.30000 111.07000
mean_percent_endocrine_area 39 1.60892 0.84861 62.74772 0.27047 4.06652
mean_percent_acinar_area 39 73.94779 4.69373 2884 61.44842 82.42857
mean_percent_remaining_area 39 24.44330 4.94532 953.28855 15.93143 37.64155

Pearson Correlations

Pearson Correlation Coefficients
Prob > |r| under H0: Rho=0
Number of Observations
  oppc_c_peptideR1 endocrine_weight1 acinar_weight1 remaining_weight1 total_weight1 mean_percent_endocrine_area mean_percent_acinar_area mean_percent_remaining_area
oppc_c_peptideR1
1.00000
 
33
0.64885
<.0001
33
0.25524
0.1517
33
0.28631
0.1062
33
0.27776
0.1176
33
0.60919
0.0002
33
0.00083
0.9963
33
-0.12542
0.4868
33
endocrine_weight1
0.64885
<.0001
33
1.00000
 
34
0.69341
<.0001
34
0.59414
0.0002
34
0.69431
<.0001
34
0.69161
<.0001
34
0.28910
0.0973
34
-0.40244
0.0183
34
acinar_weight1
0.25524
0.1517
33
0.69341
<.0001
34
1.00000
 
34
0.90706
<.0001
34
0.99542
<.0001
34
0.03223
0.8564
34
0.40011
0.0190
34
-0.38661
0.0239
34
remaining_weight1
0.28631
0.1062
33
0.59414
0.0002
34
0.90706
<.0001
34
1.00000
 
34
0.94255
<.0001
34
-0.08222
0.6439
34
0.01240
0.9445
34
0.00334
0.9850
34
total_weight1
0.27776
0.1176
33
0.69431
<.0001
34
0.99542
<.0001
34
0.94255
<.0001
34
1.00000
 
34
0.02216
0.9010
34
0.31856
0.0663
34
-0.30716
0.0772
34
mean_percent_endocrine_area
0.60919
0.0002
33
0.69161
<.0001
34
0.03223
0.8564
34
-0.08222
0.6439
34
0.02216
0.9010
34
1.00000
 
39
0.21401
0.1908
39
-0.37473
0.0188
39
mean_percent_acinar_area
0.00083
0.9963
33
0.28910
0.0973
34
0.40011
0.0190
34
0.01240
0.9445
34
0.31856
0.0663
34
0.21401
0.1908
39
1.00000
 
39
-0.98585
<.0001
39
mean_percent_remaining_area
-0.12542
0.4868
33
-0.40244
0.0183
34
-0.38661
0.0239
34
0.00334
0.9850
34
-0.30716
0.0772
34
-0.37473
0.0188
39
-0.98585
<.0001
39
1.00000
 
39

statistical analysis for figure 3b

In [125]:
proc mixed data=weight1;
class donor_group_specific npodCaseID;
model endocrine_weight=donor_group_specific /solution ddfm = kenwardroger;
random int/ subject=nPODCaseid;
lsmeans donor_group_specific/adjust=tukey cl pdiff alpha=0.05;
/*parms/ols does not fix the problem that the convergence criteria was met but final hessian is not positive definitive.  This warning is caused
by the magnitidue of the numbers (very small).*/
run;
Out[125]:
SAS Output

SAS Output

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.WEIGHT1
Dependent Variable endocrine_weight
Covariance Structure Variance Components
Subject Effect nPODCaseID
Estimation Method REML
Residual Variance Method Profile
Fixed Effects SE Method Kenward-Roger
Degrees of Freedom Method Kenward-Roger

Class Level Information

Class Level Information
Class Levels Values
donor_group_specific 4 AAb+ ND T1D INS+ T1D INS-
nPODCaseID 34 6062 6064 6079 6087 6089 6195 6197 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6421 6424 6429 6445 6450

Dimensions

Dimensions
Covariance Parameters 2
Columns in X 5
Columns in Z per Subject 1
Subjects 34
Max Obs per Subject 1

Number of Observations

Number of Observations
Number of Observations Read 39
Number of Observations Used 34
Number of Observations Not Used 5

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 -365.71398353  
1 1 -365.71398353 0.00000000

Convergence Status

Convergence criteria met but final hessian is not positive definite.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Intercept nPODCaseID 5.03E-14
Residual   2.243E-7

Fit Statistics

Fit Statistics
-2 Res Log Likelihood -365.7
AIC (Smaller is Better) -361.7
AICC (Smaller is Better) -361.3
BIC (Smaller is Better) -358.7

Solution for Fixed Effects

Solution for Fixed Effects
Effect donor_group_specific Estimate Standard
Error
DF t Value Pr > |t|
Intercept   0.000528 0.000179 30 2.95 0.0061
donor_group_specific AAb+ 0.001094 0.000253 30 4.32 0.0002
donor_group_specific ND 0.001582 0.000225 30 7.02 <.0001
donor_group_specific T1D INS+ -0.00004 0.000245 30 -0.17 0.8692
donor_group_specific T1D INS- 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
donor_group_specific 3 30 26.83 <.0001

Least Squares Means

Least Squares Means
Effect donor_group_specific Estimate Standard
Error
DF t Value Pr > |t| Alpha Lower Upper
donor_group_specific AAb+ 0.001622 0.000179 30 9.06 <.0001 0.05 0.001256 0.001987
donor_group_specific ND 0.002110 0.000137 30 15.43 <.0001 0.05 0.001831 0.002389
donor_group_specific T1D INS+ 0.000487 0.000167 30 2.91 0.0067 0.05 0.000145 0.000829
donor_group_specific T1D INS- 0.000528 0.000179 30 2.95 0.0061 0.05 0.000162 0.000894

Differences of Least Squares Means

Differences of Least Squares Means
Effect donor_group_specific _donor_group_specific Estimate Standard
Error
DF t Value Pr > |t| Adjustment Adj P Alpha Lower Upper Adj Lower Adj Upper
donor_group_specific AAb+ ND -0.00049 0.000225 30 -2.17 0.0381 Tukey 0.1551 0.05 -0.00095 -0.00003 -0.00110 0.000124
donor_group_specific AAb+ T1D INS+ 0.001134 0.000245 30 4.63 <.0001 Tukey 0.0004 0.05 0.000634 0.001635 0.000468 0.001801
donor_group_specific AAb+ T1D INS- 0.001094 0.000253 30 4.32 0.0002 Tukey 0.0009 0.05 0.000577 0.001611 0.000405 0.001782
donor_group_specific ND T1D INS+ 0.001623 0.000216 30 7.51 <.0001 Tukey <.0001 0.05 0.001181 0.002064 0.001035 0.002211
donor_group_specific ND T1D INS- 0.001582 0.000225 30 7.02 <.0001 Tukey <.0001 0.05 0.001122 0.002042 0.000970 0.002195
donor_group_specific T1D INS+ T1D INS- -0.00004 0.000245 30 -0.17 0.8692 Tukey 0.9983 0.05 -0.00054 0.000460 -0.00071 0.000626
In [126]:
proc mixed data=weight1;
class donor_group_specific npodCaseID;
model acinar_weight=donor_group_specific /solution ddfm = kenwardroger;
random int/ subject=nPODCaseid;
lsmeans donor_group_specific/adjust=tukey cl pdiff alpha=0.05;
parms /ols;
run;
Out[126]:
SAS Output

SAS Output

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.WEIGHT1
Dependent Variable acinar_weight
Covariance Structure Variance Components
Subject Effect nPODCaseID
Estimation Method REML
Residual Variance Method Profile
Fixed Effects SE Method Kenward-Roger
Degrees of Freedom Method Kenward-Roger

Class Level Information

Class Level Information
Class Levels Values
donor_group_specific 4 AAb+ ND T1D INS+ T1D INS-
nPODCaseID 34 6062 6064 6079 6087 6089 6195 6197 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6421 6424 6429 6445 6450

Dimensions

Dimensions
Covariance Parameters 2
Columns in X 5
Columns in Z per Subject 1
Subjects 34
Max Obs per Subject 1

Number of Observations

Number of Observations
Number of Observations Read 39
Number of Observations Used 34
Number of Observations Not Used 5

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 -138.94934956  
1 0 -138.94934956 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Intercept nPODCaseID 0
Residual   0.000430

Fit Statistics

Fit Statistics
-2 Res Log Likelihood -138.9
AIC (Smaller is Better) -136.9
AICC (Smaller is Better) -136.8
BIC (Smaller is Better) -135.4

PARMS Model Likelihood Ratio Test

PARMS Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
0 0.00 1.0000

Solution for Fixed Effects

Solution for Fixed Effects
Effect donor_group_specific Estimate Standard
Error
DF t Value Pr > |t|
Intercept   0.04483 0.007839 30 5.72 <.0001
donor_group_specific AAb+ 0.02637 0.01109 30 2.38 0.0239
donor_group_specific ND 0.02348 0.009864 30 2.38 0.0238
donor_group_specific T1D INS+ 0.003646 0.01073 30 0.34 0.7365
donor_group_specific T1D INS- 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
donor_group_specific 3 30 3.39 0.0308

Least Squares Means

Least Squares Means
Effect donor_group_specific Estimate Standard
Error
DF t Value Pr > |t| Alpha Lower Upper
donor_group_specific AAb+ 0.07120 0.007839 30 9.08 <.0001 0.05 0.05519 0.08721
donor_group_specific ND 0.06831 0.005987 30 11.41 <.0001 0.05 0.05608 0.08054
donor_group_specific T1D INS+ 0.04847 0.007333 30 6.61 <.0001 0.05 0.03350 0.06345
donor_group_specific T1D INS- 0.04483 0.007839 30 5.72 <.0001 0.05 0.02882 0.06084

Differences of Least Squares Means

Differences of Least Squares Means
Effect donor_group_specific _donor_group_specific Estimate Standard
Error
DF t Value Pr > |t| Adjustment Adj P Alpha Lower Upper Adj Lower Adj Upper
donor_group_specific AAb+ ND 0.002891 0.009864 30 0.29 0.7715 Tukey-Kramer 0.9911 0.05 -0.01725 0.02304 -0.02393 0.02971
donor_group_specific AAb+ T1D INS+ 0.02273 0.01073 30 2.12 0.0426 Tukey-Kramer 0.1707 0.05 0.000806 0.04465 -0.00646 0.05191
donor_group_specific AAb+ T1D INS- 0.02637 0.01109 30 2.38 0.0239 Tukey-Kramer 0.1031 0.05 0.003733 0.04901 -0.00377 0.05652
donor_group_specific ND T1D INS+ 0.01984 0.009466 30 2.10 0.0447 Tukey-Kramer 0.1777 0.05 0.000504 0.03917 -0.00590 0.04558
donor_group_specific ND T1D INS- 0.02348 0.009864 30 2.38 0.0238 Tukey-Kramer 0.1027 0.05 0.003338 0.04363 -0.00334 0.05030
donor_group_specific T1D INS+ T1D INS- 0.003646 0.01073 30 0.34 0.7365 Tukey-Kramer 0.9862 0.05 -0.01828 0.02557 -0.02554 0.03283
In [127]:
proc mixed data=weight1;
class donor_group_specific npodCaseID;
model remaining_weight=donor_group_specific /solution ddfm = kenwardroger;
random int/ subject=nPODCaseid;
lsmeans donor_group_specific/adjust=tukey cl pdiff alpha=0.05;
parms /ols;
run;
Out[127]:
SAS Output

SAS Output

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.WEIGHT1
Dependent Variable remaining_weight
Covariance Structure Variance Components
Subject Effect nPODCaseID
Estimation Method REML
Residual Variance Method Profile
Fixed Effects SE Method Kenward-Roger
Degrees of Freedom Method Kenward-Roger

Class Level Information

Class Level Information
Class Levels Values
donor_group_specific 4 AAb+ ND T1D INS+ T1D INS-
nPODCaseID 34 6062 6064 6079 6087 6089 6195 6197 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6421 6424 6429 6445 6450

Dimensions

Dimensions
Covariance Parameters 2
Columns in X 5
Columns in Z per Subject 1
Subjects 34
Max Obs per Subject 1

Number of Observations

Number of Observations
Number of Observations Read 39
Number of Observations Used 34
Number of Observations Not Used 5

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 -220.61082396  
1 0 -220.61082396 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Intercept nPODCaseID 0
Residual   0.000028

Fit Statistics

Fit Statistics
-2 Res Log Likelihood -220.6
AIC (Smaller is Better) -218.6
AICC (Smaller is Better) -218.5
BIC (Smaller is Better) -217.1

PARMS Model Likelihood Ratio Test

PARMS Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
0 0.00 1.0000

Solution for Fixed Effects

Solution for Fixed Effects
Effect donor_group_specific Estimate Standard
Error
DF t Value Pr > |t|
Intercept   0.01813 0.002010 30 9.02 <.0001
donor_group_specific AAb+ 0.003445 0.002842 30 1.21 0.2350
donor_group_specific ND 0.002844 0.002529 30 1.12 0.2698
donor_group_specific T1D INS+ -0.00146 0.002752 30 -0.53 0.6007
donor_group_specific T1D INS- 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
donor_group_specific 3 30 1.57 0.2170

Least Squares Means

Least Squares Means
Effect donor_group_specific Estimate Standard
Error
DF t Value Pr > |t| Alpha Lower Upper
donor_group_specific AAb+ 0.02158 0.002010 30 10.74 <.0001 0.05 0.01747 0.02568
donor_group_specific ND 0.02098 0.001535 30 13.67 <.0001 0.05 0.01784 0.02411
donor_group_specific T1D INS+ 0.01668 0.001880 30 8.87 <.0001 0.05 0.01284 0.02052
donor_group_specific T1D INS- 0.01813 0.002010 30 9.02 <.0001 0.05 0.01403 0.02224

Differences of Least Squares Means

Differences of Least Squares Means
Effect donor_group_specific _donor_group_specific Estimate Standard
Error
DF t Value Pr > |t| Adjustment Adj P Alpha Lower Upper Adj Lower Adj Upper
donor_group_specific AAb+ ND 0.000601 0.002529 30 0.24 0.8136 Tukey-Kramer 0.9952 0.05 -0.00456 0.005766 -0.00628 0.007478
donor_group_specific AAb+ T1D INS+ 0.004901 0.002752 30 1.78 0.0851 Tukey-Kramer 0.3021 0.05 -0.00072 0.01052 -0.00258 0.01238
donor_group_specific AAb+ T1D INS- 0.003445 0.002842 30 1.21 0.2350 Tukey-Kramer 0.6242 0.05 -0.00236 0.009250 -0.00428 0.01117
donor_group_specific ND T1D INS+ 0.004300 0.002427 30 1.77 0.0866 Tukey-Kramer 0.3065 0.05 -0.00066 0.009257 -0.00230 0.01090
donor_group_specific ND T1D INS- 0.002844 0.002529 30 1.12 0.2698 Tukey-Kramer 0.6776 0.05 -0.00232 0.008009 -0.00403 0.009720
donor_group_specific T1D INS+ T1D INS- -0.00146 0.002752 30 -0.53 0.6007 Tukey-Kramer 0.9514 0.05 -0.00708 0.004165 -0.00894 0.006027

figure 3b

In [128]:
boxplot<-import("weight_long.csv")


boxplot %<>% mutate(donor_range = ifelse(donor_group_specific == "ND", "ND AAb-",
                                              ifelse(donor_group_specific == "AAb+", "ND AAb+",
                                                   ifelse(donor_group_specific == "T1D INS+", "T1D INS+",
                                                    "T1D INS-"))))

boxplot <- within(boxplot,donor_range <- factor(donor_range,
                                            levels=rev(c("T1D INS-",
                                                     "T1D INS+",
                                                         "ND AAb+",
                                                           "ND AAb-"))))


boxplot %<>% mutate(region = ifelse(tissue== "endocrine_weight", "Endocrine",
                                             ifelse(tissue == "acinar_weight", "Acinar",
                                                 "Ductal/Other")))
                                                    

# for reordering the columns
boxplot <- within(boxplot,region <- factor(region,
                                            levels=rev(c("Ductal/Other",
                                                     "Acinar",
                                                     "Endocrine"))))


boxplot <- boxplot[boxplot$region == "Endocrine",]

#boxplots defaults used, i.e. box represents IQR, whiskers 1.5*IQR, beyond whiskers are outliers, and line within box is the median.  
fig<-ggplot(boxplot, aes(region,COL1)) +
geom_boxplot(outlier.size=NA, outlier.color=NA, color="black", alpha=0.3, show.legend=FALSE, color=boxplot$donor_range, aes(fill=donor_range)) +
scale_color_manual(guide = FALSE, values =c("#1B9E77", "#D95F02", "#7570B3", "#E7298A")) + #comment this line out if you want to use R's auto-color palette
scale_fill_manual(guide = FALSE, values=c("ND AAb-" = "#1B9E77", "ND AAb+" = "#D95F02", "T1D INS+" = "#7570B3", "T1D INS-" = "#E7298A")) +  #comment this line out if you want to use R's auto-color palette

geom_jitter(aes(region,COL1, color=boxplot$donor_range, group=donor_range),
        position=position_jitterdodge(jitter.width = .25),   
        alpha=.4,
        size=2.5,
        show.legend=FALSE)+

#geom_point(aes(region,COL1, color=donor_range, group=donor_range), 
#           position = position_dodge(width=.75),
#          alpha=0.5,
#          size=3,
#          show.legend=FALSE) +


    xlab("") +
    ylab("Tissue weight\n (% of Body Weight)") +
theme(axis.title = element_text(size=15,color='black', family="Arial", face="bold"),
          axis.text.y = element_text(size=15,color='black', family="Arial"), 
          axis.text.x=element_text (size=15,color='black', family="Arial", face="bold"),
          axis.ticks=element_line(color="black"),
          panel.background=element_blank())+
     panel_border(colour = "black", size = 0.5, linetype = 1, remove = FALSE)+
     geom_signif(y_position=c(0.0033, 0.0036, 0.0039, 0.0042), xmin=c(.9, .9, .7, .7), xmax=c(1.1, 1.25, 1.1, 1.25),
     annotation=c("**", "**", "***", "***"), tip_length=0, size=.75, textsize=6, color="black", vjust=0.45) + #see here https://rdrr.io/cran/ggsignif/man/stat_signif.html

     geom_signif(y_position=c(0.0045), xmin=c(.50), xmax=c(1.50),
     annotation=c( "***"), tip_length=.025, size=.75, textsize=6, color="black", vjust=0.45) +
scale_y_continuous(limits = c(0, 0.0050), breaks=c(0,0.0025, 0.0050)) 




fig 

save_plot("fig3b_1.tiff", fig, base_aspect_ratio=1/.90)
Warning message:
"Duplicated aesthetics after name standardisation: colour"
Warning message:
"Use of `boxplot$donor_range` is discouraged. Use `donor_range` instead."
Warning message in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
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In [129]:
boxplot<-import("weight_long.csv")


boxplot %<>% mutate(donor_range = ifelse(donor_group_specific == "ND", "ND AAb-",
                                              ifelse(donor_group_specific == "AAb+", "ND AAb+",
                                                   ifelse(donor_group_specific == "T1D INS+", "T1D INS+",
                                                    "T1D INS-"))))

boxplot <- within(boxplot,donor_range <- factor(donor_range,
                                            levels=rev(c("T1D INS-",
                                                     "T1D INS+",
                                                         "ND AAb+",
                                                           "ND AAb-"))))


boxplot %<>% mutate(region = ifelse(tissue== "endocrine_weight", "Endocrine",
                                             ifelse(tissue == "acinar_weight", "Acinar",
                                                 "Ductal/Other")))
                                                    

# for reordering the columns
boxplot <- within(boxplot,region <- factor(region,
                                            levels=rev(c("Ductal/Other",
                                                     "Acinar",
                                                     "Endocrine"))))

boxplot <- boxplot[boxplot$region == "Acinar",]
#boxplots defaults used, i.e. box represents IQR, whiskers 1.5*IQR, beyond whiskers are outliers, and line within box is the median.  
fig<-ggplot(boxplot, aes(region,COL1)) +
geom_boxplot(outlier.size=NA, outlier.color=NA, color="black", alpha=0.3, show.legend=FALSE, color=boxplot$donor_range, aes(fill=donor_range)) +
scale_color_manual(guide = FALSE, values =c("#1B9E77", "#D95F02", "#7570B3", "#E7298A")) + #comment this line out if you want to use R's auto-color palette
scale_fill_manual(guide = FALSE, values=c("ND AAb-" = "#1B9E77", "ND AAb+" = "#D95F02", "T1D INS+" = "#7570B3", "T1D INS-" = "#E7298A")) +  #comment this line out if you want to use R's auto-color palette

geom_jitter(aes(region,COL1, color=boxplot$donor_range, group=donor_range),
        position=position_jitterdodge(jitter.width = .25),   
        alpha=.4,
        size=2.5,
        show.legend=FALSE)+

#geom_point(aes(region,COL1, color=donor_range, group=donor_range), 
#           position = position_dodge(width=.75),
#          alpha=0.5,
#          size=3,
#          show.legend=FALSE) +


    xlab("") +
    ylab("Tissue weight\n (% of Body Weight)") +
theme(axis.title = element_text(size=15,color='black', family="Arial", face="bold"),
          axis.text.y = element_text(size=15,color='black', family="Arial"), 
          axis.text.x=element_text (size=15,color='black', family="Arial", face="bold"),
          axis.ticks=element_line(color="black"),
          panel.background=element_blank())+
     panel_border(colour = "black", size = 0.5, linetype = 1, remove = FALSE)+
     geom_signif(y_position=c(0.14), xmin=c(.50), xmax=c(1.50),
     annotation=c( "*"), tip_length=.025, size=.75, textsize=6, color="black", vjust=0.45) +

scale_y_continuous(limits = c(0, 0.15), breaks=c(0, 0.05, 0.1, 0.15)) 




fig 

save_plot("fig3b_2.tiff", fig, base_aspect_ratio=1/.90)
Warning message:
"Duplicated aesthetics after name standardisation: colour"
Warning message:
"Use of `boxplot$donor_range` is discouraged. Use `donor_range` instead."
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In [130]:
boxplot<-import("weight_long.csv")


boxplot %<>% mutate(donor_range = ifelse(donor_group_specific == "ND", "ND AAb-",
                                              ifelse(donor_group_specific == "AAb+", "ND AAb+",
                                                   ifelse(donor_group_specific == "T1D INS+", "T1D INS+",
                                                    "T1D INS-"))))

boxplot <- within(boxplot,donor_range <- factor(donor_range,
                                            levels=rev(c("T1D INS-",
                                                     "T1D INS+",
                                                         "ND AAb+",
                                                           "ND AAb-"))))


boxplot %<>% mutate(region = ifelse(tissue== "endocrine_weight", "Endocrine",
                                             ifelse(tissue == "acinar_weight", "Acinar",
                                                 "Ductal/Other")))
                                                    

# for reordering the columns
boxplot <- within(boxplot,region <- factor(region,
                                            levels=rev(c("Ductal/Other",
                                                     "Acinar",
                                                     "Endocrine"))))

boxplot <- boxplot[boxplot$region == "Ductal/Other",]
#boxplots defaults used, i.e. box represents IQR, whiskers 1.5*IQR, beyond whiskers are outliers, and line within box is the median.  
fig<-ggplot(boxplot, aes(region,COL1)) +
geom_boxplot(outlier.size=NA, outlier.color=NA, color="black", alpha=0.3, show.legend=FALSE, color=boxplot$donor_range, aes(fill=donor_range)) +
scale_color_manual(guide = FALSE, values =c("#1B9E77", "#D95F02", "#7570B3", "#E7298A")) + #comment this line out if you want to use R's auto-color palette
scale_fill_manual(guide = FALSE, values=c("ND AAb-" = "#1B9E77", "ND AAb+" = "#D95F02", "T1D INS+" = "#7570B3", "T1D INS-" = "#E7298A")) +  #comment this line out if you want to use R's auto-color palette

geom_jitter(aes(region,COL1, color=boxplot$donor_range, group=donor_range),
        position=position_jitterdodge(jitter.width = .25),   
        alpha=.4,
        size=2.5,
        show.legend=FALSE)+

#geom_point(aes(region,COL1, color=donor_range, group=donor_range), 
#           position = position_dodge(width=.75),
#          alpha=0.5,
#          size=3,
#          show.legend=FALSE) +


    xlab("") +
    ylab("Tissue weight\n (% of Body Weight)") +
theme(axis.title = element_text(size=15,color='black', family="Arial", face="bold"),
          axis.text.y = element_text(size=15,color='black', family="Arial"), 
          axis.text.x=element_text (size=15,color='black', family="Arial", face="bold"),
          axis.ticks=element_line(color="black"),
          panel.background=element_blank())+
     panel_border(colour = "black", size = 0.5, linetype = 1, remove = FALSE)+
     geom_signif(y_position=c(42, 48), xmin=c( 0.7, 0.9), xmax=c(1.28, 1.28),
     annotation=c( "*", "*"), tip_length=0, size=.75, textsize=6, color="black", vjust=0.45) + #see here https://rdrr.io/cran/ggsignif/man/stat_signif.html
scale_y_continuous(limits = c(0, 0.05), breaks=c(0,0.025, 0.05)) 




fig 

save_plot("fig3b_3.tiff", fig, base_aspect_ratio=1/.90)
Warning message:
"Duplicated aesthetics after name standardisation: colour"
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Figure 3a

figure 3a: main effects visualization - differences in endocrine, acinar, ductal cell area by donortype. Statistics for this figure are in the supplemental figure 1 section

In [131]:
lollipop<-import("cell3_lollipop.csv")

lollipop %<>% mutate(donorgroup1 = ifelse(donorgroup == "No diabetes", "ND AAb-",
                                       ifelse(donorgroup == "Autoab Pos", "ND AAb+",
                                              ifelse(donorgroup == "Ins. pos. T1D", "T1D INS+",
                                                    "T1D INS-"))))

#lollipop <- within(lollipop,donorgroup1 <- factor(donorgroup1,
#                                            levels=rev(c("T1D INS-",
#                                                     "T1D INS+",
#                                                     "ND AAb+",
#                                                        "ND AAb-"))))


endocrine<-ggdotchart (lollipop, x="donorgroup1", y="group_percent_endocrine_area",
            color=c("#1B9E77", "#D95F02", "#7570B3", "#E7298A"), #color
            palette=c("#1B9E77", "#D95F02", "#7570B3", "#E7298A"), #color
            add="segments", #line to lollipop
            add.params = list(color = c("black"), size = 1), #line color
            label = round(lollipop$group_percent_endocrine_area,1), font.label = list(color = "white", size = 20, vjust=0.5, face = "bold"), #label 
            rotate=TRUE, #rotate from vertical to horizonal
            dot.size=20, #change dote size
            xlab=TRUE, ylab=FALSE, #hide label
            ggtheme=theme(legend.position = "none",legend.text=element_text(size=18, face="bold", family="Arial"), legend.title=element_text(size=20, face="bold", family="Arial"),
            axis.text=element_text(size=26, color="black", family="Arial", face="bold"), 
            axis.title.x=element_text(size=26, face="bold", family="Arial"), axis.ticks.x=element_blank(), 
            aspect.ratio=.54, panel.background = element_blank()))+
            panel_border(colour = "black", size = 1, linetype = 1, remove = FALSE) +
        scale_x_discrete(limits=c("ND AAb-", "ND AAb+", "T1D INS+", "T1D INS-"), labels=c("ND AAb-","ND AAb+","T1D INS+","T1D INS-")) +
        scale_y_continuous(name=" Endocrine Area (%)", limits=c(0,3.3), labels=c()) +
#geom_shadowtext(label=round(lollipop$group_percent_endocrine_area,1), color = "white", size = 7, vjust=0.5, face = "bold")
     geom_signif(y_position=c(2.6, 2.8, 3.0, 3.2), xmin=c(2,2, 1, 1),xmax=c(3,4, 3,4),
              annotation=c("**", "**", "***","***"), tip_length=0, size=1, color="black", textsize=10) #see here https://rdrr.io/cran/ggsignif/man/stat_signif.html

endocrine
save_plot("fig3a1.tiff", endocrine, base_aspect_ratio=1.7)

acinar<-ggdotchart (lollipop, x="donorgroup1", y="group_percent_acinar_area",
            color=c("#D95F02", "#1B9E77", "#7570B3", "#E7298A"), #color
             palette=c("#D95F02", "#1B9E77", "#7570B3", "#E7298A"), #color
             add="segments", #line to lollipop
            add.params = list(color = c("black"), size = 1), #line color
              label = round(lollipop$group_percent_acinar_area,1), font.label = list(color = "white", size = 20, vjust=0.5, face = "bold"), #label 
            rotate=TRUE, #rotate from vertical to horizonal
            dot.size=20, #change dote size
            xlab=TRUE, ylab=FALSE, #hide label
            ggtheme=theme(legend.position = "none",legend.text=element_text(size=18, face="bold", family="Arial"), legend.title=element_text(size=20, face="bold", family="Arial"),
            axis.text=element_text(size=26, color="black", family="Arial", face="bold"), 
            axis.title.x=element_text(size=26, face="bold", family="Arial"), axis.ticks.x=element_blank(), 
            aspect.ratio=.54, panel.background = element_blank()))+
            panel_border(colour = "black", size = 1, linetype = 1, remove = FALSE) +
        scale_x_discrete(limits=c("ND AAb-", "ND AAb+", "T1D INS+", "T1D INS-"), labels=c("ND AAb-","ND AAb+","T1D INS+","T1D INS-")) +
        scale_y_continuous(name="Acinar Area (%)", limits=c(0, 92), labels=c())+
#geom_shadowtext(label=round(lollipop$group_percent_acinar_area,1), color = "white", size = 7, vjust=0.5, face = "bold")
        geom_signif(comparisons=list(c("ND AAb+", "T1D INS-")),
                      y_position = 84, annotation=c("*"), tip_length=0, size=1, color="black", textsize=10) +
        geom_signif(comparisons=list(c("ND AAb-", "T1D INS-")),
                      y_position = 90, annotation=c("*"), tip_length=0, size=1, color="black", textsize=10) 

acinar
save_plot("fig3a2.tiff", acinar, base_aspect_ratio=1.7)

remaining<-ggdotchart (lollipop, x="donorgroup1", y="group_percent_remaining_area",
            color=c("#E7298A", "#7570B3", "#D95F02", "#1B9E77"), #color
            palette=c("#E7298A", "#7570B3", "#D95F02", "#1B9E77"), #color
            add="segments", #line to lollipop
            add.params = list(color = c("black"), size = 1), #line color
            label = round(lollipop$group_percent_remaining_area,1), font.label = list(color = "white", size = 20, vjust=0.5, face = "bold"), #label 
            rotate=TRUE, #rotate from vertical to horizonal
            dot.size=20, #change dote size
            xlab=TRUE, ylab=FALSE, #hide label
            ggtheme=theme(legend.position = "none",legend.text=element_text(size=18, face="bold", family="Arial"), legend.title=element_text(size=20, face="bold", family="Arial"),
            axis.text=element_text(size=26, color="black", family="Arial", face="bold"), 
            axis.title.x=element_text(size=26, face="bold", family="Arial"), axis.ticks.x=element_blank(), 
            aspect.ratio=.54, panel.background = element_blank()))+
            panel_border(colour = "black", size = 1, linetype = 1, remove = FALSE) +
         scale_x_discrete(limits=c("ND AAb-", "ND AAb+", "T1D INS+", "T1D INS-"), labels=c("ND AAb-","ND AAb+","T1D INS+","T1D INS-")) +
        scale_y_continuous(name="Ductal/Other Area (%)", limits=c(0,37.4), labels=c()) +
        #geom_shadowtext(label=round(lollipop$group_percent_remaining_area,1), color = "white", size = 7, vjust=0.5, face = "bold")
        geom_signif(comparisons=list(c("ND AAb+", "T1D INS-")),
                      y_position = 33.8, annotation=c("*"), tip_length=0, size=1, color="black", textsize=10) +
        geom_signif(comparisons=list(c("ND AAb-", "T1D INS-")),
                      y_position = 36.4, annotation=c("**"), tip_length=0, size=1, color="black", textsize=10) 

remaining
save_plot("fig3a3.tiff", remaining, base_aspect_ratio=1.7)

                       
fig2a<-plot_grid(endocrine, acinar, remaining, nrow=1, ncol=3, 
                labels="A", 
                label_size=40,
               label_x=0,
               label_y=1)





#features like expand=() expand_limits()  expand=expand_scale()

save_plot("fig3a.tiff", fig2a, ncol=3, nrow=1, base_aspect_ratio=1.7)
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Figure 4

In [132]:
bubble <- import("cell3.csv")

bubble = bubble[!duplicated(bubble$nPODCaseID),]

#Recode and order the variables
bubble %<>% mutate(donor_range = ifelse(donorgroup == "No diabetes", "ND AAb-",
                                       ifelse(donorgroup == "Autoab Pos", "ND AAb+",
                                              ifelse(donorgroup == "Ins. pos. T1D", "T1D INS+",
                                                    "T1D INS-"))))

bubble <- within(bubble,donor_range <- factor(donor_range,
                                            levels=rev(c("T1D INS-",
                                                     "T1D INS+",
                                                     "ND AAb+",
                                                        "ND AAb-"))))



p<-ggplot(bubble,aes(x=donor_range, y=mean_endocrine_density, color=donor_range, size=mean_endocrine_cell_size_scale1)) + 
scale_color_manual(guide = FALSE, values =c("#1B9E77", "#D95F02", "#7570B3", "#E7298A")) + #comment this line out if you want to use R's auto-color palette
scale_fill_manual(guide = FALSE, values=c("No diabetes" = "#1B9E77", "ND AAb+" = "#D95F02", "T1D INS+" = "#7570B3", "T1D INS-" = "#E7298A")) +  #comment this line out if you want to use R's auto-color palette
geom_quasirandom(inherit.aes=TRUE, alpha=0.65, width=.6) + #width= to increase spread
theme (aspect.ratio=1/1)+
  ylab("Endocrine density\n(cells/mm2)") +
  xlab("") +
  # replace none with the following to add the legend back into the figure: c(.785,.90)    
  theme(legend.position="bottom", legend.text=element_text(size=12, face="bold", family="Arial"), legend.title=element_text(size=12, face="bold", family="Arial"),
        axis.text=element_text(size=20, color="black", family="Arial"), axis.title=element_text(size=22, face="bold", family="Arial", color="black"), axis.ticks=element_line(color="black"),
      panel.background=element_blank(), panel.border = element_rect(color = "black", fill=NA, size=.5, linetype=1)) +
scale_y_continuous(limits=c(5000,16000))+
        geom_signif(comparisons=list(c("ND AAb+", "T1D INS-")),
                      y_position = 12700, annotation=c("*"), tip_length=0, size=.75,  color="black", textsize=10)+
        geom_signif(comparisons=list(c("ND AAb+", "T1D INS+")),
                      y_position = 13700, annotation=c("**"), tip_length=0, size=.75,color="black", textsize=10)+
        geom_signif(comparisons=list(c("ND AAb-", "T1D INS-")),
                      y_position = 14700, annotation=c("**"), tip_length=0, size=.75, color="black", textsize=10)+
        geom_signif(comparisons=list(c("ND AAb-", "T1D INS+")),
                      y_position = 15700, annotation=c("**"), tip_length=0, size=.75, color="black", textsize=10)+
scale_size_continuous(limits=c(0.1,20), breaks=c(5,10,20))



fig4a<-p+labs(size="Cell size scale") + guides(size=guide_legend(nrow=1))  + theme(legend.key=element_blank()) 


fig4a

#save_plot("fig6.tiff", fig6, base_aspect_ratio=5/1)
ggsave("fig4a.png", fig4a,  height = 7, width = 7, units="in", dpi = 500, scale=1)
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In [133]:
bubble <- import("cell3.csv")
bubble = bubble[!duplicated(bubble$nPODCaseID),]
#Recode and order the variables
bubble %<>% mutate(donor_range = ifelse(donorgroup == "No diabetes", "ND AAb-",
                                       ifelse(donorgroup == "Autoab Pos", "ND AAb+",
                                              ifelse(donorgroup == "Ins. pos. T1D", "T1D INS+",
                                                    "T1D INS-"))))

bubble <- within(bubble,donor_range <- factor(donor_range,
                                            levels=rev(c("T1D INS-",
                                                     "T1D INS+",
                                                     "ND AAb+",
                                                        "ND AAb-"))))

p<-ggplot(bubble,aes(x=donor_range, y=mean_acinar_density, color=donor_range, size=mean_acinar_cell_size_scale1)) + 
scale_color_manual(guide = FALSE, values =c("#1B9E77", "#D95F02", "#7570B3", "#E7298A")) + #comment this line out if you want to use R's auto-color palette
scale_fill_manual(guide = FALSE, values=c("No diabetes" = "#1B9E77", "ND AAb+" = "#D95F02", "T1D INS+" = "#7570B3", "T1D INS-" = "#E7298A")) +  #comment this line out if you want to use R's auto-color palette

#scale_size_continuous(range=c(0.1, 10)) +
geom_quasirandom(inherit.aes=TRUE, alpha=0.65, width=0.5) +
  ylab("Acinar density\n(cells/mm2)") +
  xlab("") +
  # replace none with the following to add the legend back into the figure: c(.785,.90)    
  theme(aspect.ratio=1/1, legend.position="bottom", legend.text=element_text(size=12, face="bold", family="Arial"), legend.title=element_text(size=12, face="bold", family="Arial"),
        axis.text=element_text(size=20, color="black", family="Arial"), axis.title=element_text(size=24, face="bold", family="Arial", color="black"), axis.ticks=element_line(color="black"),
        panel.background=element_blank(), panel.border = element_rect(color = "black", fill=NA, size=.5, linetype=1)) +
scale_y_continuous(limits=c(5000,16000))+
        geom_signif(comparisons=list(c("ND AAb-", "T1D INS+")),
                      y_position = 12700, annotation=c("*"), tip_length=0, size=.75, color="black", textsize=10)+
scale_size_continuous(limits=c(0.1,20), breaks=c(5,10,20))

fig4b<-p+labs(size="Cell size scale") + guides(size=guide_legend(nrow=1)) + theme(legend.key=element_blank())


fig4b

#save_plot("fig3b.tiff", fig3b, base_aspect_ratio=1)
ggsave("fig4b.png", fig4b,  height = 7, width = 7, units="in", dpi = 500)
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In [134]:
fig4<-plot_grid(fig4a, fig4b, nrow=1, ncol=2, 
                #labels="A", 
                label_size=30,
               label_x=0,
               label_y=1)





#features like expand=() expand_limits()  expand=expand_scale()
ggsave("fig4.tiff", fig4, dpi = 300, height=15, width=15)
#save_plot("fig3.tiff", fig3, ncol=2, nrow=1, base_aspect_ratio=.9/1)
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In [135]:
%explore(endocrine_density);
Out[135]:
SAS Output

SAS Output

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable endocrine_density
Covariance Structure Variance Components
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method Parameter
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 1
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 1781.81444802  
1 1 1781.81444802 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
region nPODCaseI(donorgrou) 1472002

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 1781.8
AIC (Smaller is Better) 1783.8
AICC (Smaller is Better) 1783.9
BIC (Smaller is Better) 1785.5

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
0 0.00 1.0000

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     8709.27 324.26 35 26.86 <.0001
region   PB 382.21 467.30 68 0.82 0.4163
region   PH 305.40 458.57 68 0.67 0.5077
region   PT 0 . . . .
donorgroup Autoab Pos   524.60 537.72 35 0.98 0.3360
donorgroup Ins. neg. T1D   1514.35 561.63 35 2.70 0.0107
donorgroup Ins. pos. T1D   2277.71 502.34 35 4.53 <.0001
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB -495.89 765.75 68 -0.65 0.5194
donorgroup*region Autoab Pos PH -302.21 777.54 68 -0.39 0.6987
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB 161.57 799.34 68 0.20 0.8404
donorgroup*region Ins. neg. T1D PH 373.41 794.27 68 0.47 0.6398
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 41.1428 716.08 68 0.06 0.9544
donorgroup*region Ins. pos. T1D PH -948.84 710.41 68 -1.34 0.1861
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 0.62 0.5393
donorgroup 3 35 20.47 <.0001
donorgroup*region 6 68 0.74 0.6171

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable endocrine_density
Covariance Structure Compound Symmetry
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method Profile
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 2
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 1781.81444802  
1 2 1753.68203343 0.00000001

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
CS nPODCaseI(donorgrou) 793431
Residual   674354

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 1753.7
AIC (Smaller is Better) 1757.7
AICC (Smaller is Better) 1757.8
BIC (Smaller is Better) 1761.0

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
1 28.13 <.0001

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     8709.27 323.79 35 26.90 <.0001
region   PB 324.03 318.34 68 1.02 0.3124
region   PH 305.40 310.38 68 0.98 0.3286
region   PT 0 . . . .
donorgroup Autoab Pos   524.60 536.95 35 0.98 0.3353
donorgroup Ins. neg. T1D   1514.35 560.83 35 2.70 0.0106
donorgroup Ins. pos. T1D   2277.71 501.62 35 4.54 <.0001
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB -437.71 519.55 68 -0.84 0.4025
donorgroup*region Autoab Pos PH -344.32 530.28 68 -0.65 0.5183
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB 219.76 542.23 68 0.41 0.6865
donorgroup*region Ins. neg. T1D PH 373.41 537.60 68 0.69 0.4897
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 99.3270 486.02 68 0.20 0.8387
donorgroup*region Ins. pos. T1D PH -948.84 480.84 68 -1.97 0.0525
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 1.25 0.2940
donorgroup 3 35 10.16 <.0001
donorgroup*region 6 68 1.63 0.1530

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable endocrine_density
Covariance Structure Unstructured
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 6
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 1781.81444802  
1 2 1743.43119411 0.00000005
2 1 1743.43115867 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
UN(1,1) nPODCaseI(donorgrou) 2203465
UN(2,1) nPODCaseI(donorgrou) 773840
UN(2,2) nPODCaseI(donorgrou) 886967
UN(3,1) nPODCaseI(donorgrou) 1039947
UN(3,2) nPODCaseI(donorgrou) 590954
UN(3,3) nPODCaseI(donorgrou) 1334049

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 1743.4
AIC (Smaller is Better) 1755.4
AICC (Smaller is Better) 1756.3
BIC (Smaller is Better) 1765.4

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
5 38.38 <.0001

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     8709.27 308.69 35 28.21 <.0001
region   PB 294.37 333.03 35 0.88 0.3828
region   PH 305.40 272.44 35 1.12 0.2699
region   PT 0 . . . .
donorgroup Autoab Pos   524.60 511.90 35 1.02 0.3125
donorgroup Ins. neg. T1D   1514.35 534.67 35 2.83 0.0076
donorgroup Ins. pos. T1D   2277.71 478.22 35 4.76 <.0001
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB -408.05 541.40 35 -0.75 0.4561
donorgroup*region Autoab Pos PH -330.83 462.62 35 -0.72 0.4793
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB 249.41 564.92 35 0.44 0.6616
donorgroup*region Ins. neg. T1D PH 373.41 471.87 35 0.79 0.4341
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 128.98 506.62 35 0.25 0.8005
donorgroup*region Ins. pos. T1D PH -948.84 422.06 35 -2.25 0.0310
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 35 1.02 0.3704
donorgroup 3 35 10.14 <.0001
donorgroup*region 6 35 1.81 0.1251

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable endocrine_density
Covariance Structure Unstructured using Correlations
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 6
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 1781.81444802  
1 2 1743.43416455 0.00000389
2 1 1743.43411063 0.00000382
3 1 1743.43411062 0.00000382
4 0 1743.43411062 0.00000382
5 0 1743.43411062 0.00000382
6 1 1743.43411062 0.00000382
7 1 1743.43411058 0.00000382
8 1 1743.43411017 0.00000382
9 1 1743.43410610 0.00000382
10 1 1743.43406588 0.00000376
11 1 1743.43370796 0.00000330
12 1 1743.43350756 0.00000303
13 1 1743.43332540 0.00000280
14 1 1743.43315979 0.00000258
15 1 1743.43300917 0.00000239
16 1 1743.43287213 0.00000221
17 1 1743.43274741 0.00000205
18 1 1743.43263385 0.00000190
19 1 1743.43253040 0.00000177
20 1 1743.43243611 0.00000164
21 1 1743.43235013 0.00000153
22 1 1743.43227169 0.00000143
23 1 1743.43220006 0.00000134
24 1 1743.43213463 0.00000125
25 1 1743.43207481 0.00000118
26 1 1743.43202007 0.00000111
27 1 1743.43196995 0.00000104
28 1 1743.43192402 0.00000098
29 1 1743.43188189 0.00000093
30 1 1743.43184321 0.00000088
31 1 1743.43180766 0.00000083
32 1 1743.43177495 0.00000079
33 1 1743.43174483 0.00000075
34 1 1743.43171705 0.00000072
35 1 1743.43169142 0.00000068
36 1 1743.43166772 0.00000065
37 1 1743.43164579 0.00000062
38 1 1743.43162548 0.00000060
39 1 1743.43160663 0.00000057
40 1 1743.43158912 0.00000055
41 1 1743.43157282 0.00000053
42 1 1743.43155764 0.00000051
43 1 1743.43154348 0.00000049
44 1 1743.43153025 0.00000048
45 1 1743.43151786 0.00000046
46 1 1743.43150626 0.00000045
47 1 1743.43149536 0.00000043
48 1 1743.43148512 0.00000042
49 1 1743.43147548 0.00000041
50 1 1743.43146639 0.00000039

Convergence Status

WARNING: Did not converge.

Covariance Parameter Values At Last Iteration

Covariance Parameter Values At Last Iteration
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 2194860
Var(2) nPODCaseI(donorgrou) 887230
Var(3) nPODCaseI(donorgrou) 1333352
Corr(2,1) nPODCaseI(donorgrou) 0.5530
Corr(3,1) nPODCaseI(donorgrou) 0.6060
Corr(3,2) nPODCaseI(donorgrou) 0.5430

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable endocrine_density
Covariance Structure Banded
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 6
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 45 1781.81444802  
1 44 151616380.33487 0.49999940
2 44 151616380.33487 0.49999940

Convergence Status

WARNING: Stopped because of too many likelihood evaluations.

Covariance Parameter Values At Last Iteration

Covariance Parameter Values At Last Iteration
Cov Parm Subject Estimate
UN(1,1) nPODCaseI(donorgrou) 1.0000
UN(2,1) nPODCaseI(donorgrou) 0
UN(2,2) nPODCaseI(donorgrou) 1.0000
UN(3,1) nPODCaseI(donorgrou) 0
UN(3,2) nPODCaseI(donorgrou) 0
UN(3,3) nPODCaseI(donorgrou) 1.0000

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable endocrine_density
Covariance Structure Heterogeneous Compound Symmetry
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 4
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 1781.81444802  
1 2 1743.73688324 0.00000327
2 1 1743.73642776 0.00000269
3 1 1743.73642772 0.00000269
4 0 1743.73642772 0.00000269
5 0 1743.73642772 0.00000269
6 0 1743.73642772 0.00000269
7 1 1743.73642771 0.00000269
8 1 1743.73642756 0.00000269
9 1 1743.73642604 0.00000269
10 1 1743.73641099 0.00000267
11 1 1743.73626991 0.00000249
12 1 1743.73597256 0.00000211
13 1 1743.73572902 0.00000180
14 1 1743.73552916 0.00000154
15 1 1743.73536478 0.00000133
16 1 1743.73522926 0.00000116
17 1 1743.73511724 0.00000101
18 1 1743.73502436 0.00000089
19 1 1743.73494711 0.00000079
20 1 1743.73488262 0.00000071
21 1 1743.73482857 0.00000064
22 1 1743.73478306 0.00000058
23 1 1743.73474457 0.00000053
24 1 1743.73471183 0.00000049
25 1 1743.73468383 0.00000045
26 1 1743.73465974 0.00000042
27 1 1743.73463888 0.00000039
28 1 1743.73462069 0.00000037
29 1 1743.73460473 0.00000035
30 1 1743.73459061 0.00000033
31 1 1743.73457803 0.00000032
32 1 1743.73456676 0.00000030
33 1 1743.73455657 0.00000029
34 1 1743.73454731 0.00000028
35 1 1743.73453884 0.00000026
36 1 1743.73453104 0.00000025
37 1 1743.73452381 0.00000025
38 1 1743.73451708 0.00000024
39 1 1743.73451079 0.00000023
40 1 1743.73450487 0.00000022
41 1 1743.73449929 0.00000021
42 1 1743.73449401 0.00000021
43 1 1743.73448899 0.00000020
44 1 1743.73448421 0.00000019
45 1 1743.73447965 0.00000019
46 1 1743.73447528 0.00000018
47 1 1743.73447109 0.00000018
48 1 1743.73446706 0.00000017
49 1 1743.73446319 0.00000017
50 1 1743.73445946 0.00000016

Convergence Status

WARNING: Did not converge.

Covariance Parameter Values At Last Iteration

Covariance Parameter Values At Last Iteration
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 2186752
Var(2) nPODCaseI(donorgrou) 901450
Var(3) nPODCaseI(donorgrou) 1328463
CSH nPODCaseI(donorgrou) 0.5683

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable endocrine_density
Covariance Structure Huynh-Feldt
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 4
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 1781.81444802  
1 2 1745.34407556 0.00002130
2 1 1745.32704947 0.00000004
3 1 1745.32701730 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 1946473
Var(2) nPODCaseI(donorgrou) 914167
Var(3) nPODCaseI(donorgrou) 1484970
HF nPODCaseI(donorgrou) 671408

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 1745.3
AIC (Smaller is Better) 1753.3
AICC (Smaller is Better) 1753.7
BIC (Smaller is Better) 1760.0

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
3 36.49 <.0001

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     8709.27 325.68 35 26.74 <.0001
region   PB 295.43 318.50 68 0.93 0.3569
region   PH 305.40 309.70 68 0.99 0.3276
region   PT 0 . . . .
donorgroup Autoab Pos   524.60 540.08 35 0.97 0.3380
donorgroup Ins. neg. T1D   1514.35 564.10 35 2.68 0.0110
donorgroup Ins. pos. T1D   2277.71 504.55 35 4.51 <.0001
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB -409.11 518.93 68 -0.79 0.4332
donorgroup*region Autoab Pos PH -333.36 523.95 68 -0.64 0.5268
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB 248.35 541.54 68 0.46 0.6480
donorgroup*region Ins. neg. T1D PH 373.41 536.42 68 0.70 0.4887
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 127.92 485.51 68 0.26 0.7930
donorgroup*region Ins. pos. T1D PH -948.84 479.79 68 -1.98 0.0520
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 1.18 0.3133
donorgroup 3 35 10.40 <.0001
donorgroup*region 6 68 1.65 0.1465

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable endocrine_density
Covariance Structure Heterogeneous Autoregressive
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 4
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 1781.81444802  
1 2 1750.80680658 0.00001703
2 1 1750.79635075 0.00000401
3 1 1750.79633966 0.00000400
4 0 1750.79633966 0.00000400
5 0 1750.79633966 0.00000400
6 0 1750.79633966 0.00000400
7 1 1750.79633963 0.00000400
8 1 1750.79633933 0.00000400
9 1 1750.79633633 0.00000400
10 1 1750.79630658 0.00000396
11 1 1750.79602989 0.00000360
12 1 1750.79545958 0.00000285
13 1 1750.79500581 0.00000227
14 1 1750.79464502 0.00000180
15 1 1750.79435833 0.00000143
16 1 1750.79413065 0.00000113
17 1 1750.79394992 0.00000090
18 1 1750.79380651 0.00000071
19 1 1750.79369276 0.00000057
20 1 1750.79360256 0.00000045
21 1 1750.79353104 0.00000036
22 1 1750.79347434 0.00000028
23 1 1750.79342941 0.00000023
24 1 1750.79339378 0.00000018
25 1 1750.79336555 0.00000014
26 1 1750.79334316 0.00000012
27 1 1750.79332540 0.00000009
28 1 1750.79331132 0.00000007
29 1 1750.79330014 0.00000006
30 1 1750.79329126 0.00000005
31 1 1750.79328420 0.00000004
32 1 1750.79327859 0.00000003
33 1 1750.79327412 0.00000003
34 1 1750.79327055 0.00000002
35 1 1750.79326770 0.00000002
36 1 1750.79326542 0.00000002
37 1 1750.79326358 0.00000001
38 1 1750.79326211 0.00000001
39 1 1750.79326092 0.00000001
40 1 1750.79325995 0.00000001

Convergence Status

Convergence criteria met but final hessian is not positive definite.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 2192411
Var(2) nPODCaseI(donorgrou) 885615
Var(3) nPODCaseI(donorgrou) 1336518
ARH(1) nPODCaseI(donorgrou) 0.5471

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 1750.8
AIC (Smaller is Better) 1758.8
AICC (Smaller is Better) 1759.2
BIC (Smaller is Better) 1765.4

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
3 31.02 <.0001

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     8709.27 308.98 35 28.19 <.0001
region   PB 311.96 432.81 68 0.72 0.4735
region   PH 305.40 271.48 68 1.12 0.2646
region   PT 0 . . . .
donorgroup Autoab Pos   524.60 512.38 35 1.02 0.3129
donorgroup Ins. neg. T1D   1514.35 535.16 35 2.83 0.0077
donorgroup Ins. pos. T1D   2277.71 478.66 35 4.76 <.0001
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB -425.64 707.37 68 -0.60 0.5494
donorgroup*region Autoab Pos PH -337.20 459.57 68 -0.73 0.4656
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB 231.82 738.30 68 0.31 0.7545
donorgroup*region Ins. neg. T1D PH 373.41 470.21 68 0.79 0.4299
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 111.39 661.64 68 0.17 0.8668
donorgroup*region Ins. pos. T1D PH -948.84 420.57 68 -2.26 0.0273
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 0.65 0.5249
donorgroup 3 35 11.42 <.0001
donorgroup*region 6 68 2.32 0.0428

The SAS System

The PRINT Procedure

Data Set WORK.ALL

Description arh1 cs csh hf un unr vc
-2 Res Log Likelihood 1750.8 1753.7 650.3 1745.3 1743.4 650.2 1781.8
AIC (Smaller is Better) 1758.8 1757.7 658.3 1753.3 1755.4 662.2 1783.8
AICC (Smaller is Better) 1759.2 1757.8 658.7 1753.7 1756.3 663.1 1783.9
BIC (Smaller is Better) 1765.4 1761.0 665.0 1760.0 1765.4 672.2 1785.5

The SAS System

The PRINT Procedure

Data Set WORK.STATUS

Obs Reason Status pdG pdH covar
1 Convergence criteria met but final hessian is not positive definite. 0 1 0 arh(1)
2 Convergence criteria met. 0 1 1 cs
3 WARNING: Did not converge. 1 1 1 csh
4 Convergence criteria met. 0 1 1 hf
5 Convergence criteria met. 0 1 1 un
6 WARNING: Stopped because of too many likelihood evaluations. 1 1 1 un1
7 WARNING: Did not converge. 1 1 1 unr
8 Convergence criteria met. 0 1 1 vc
In [136]:
PROC mixed data=cell3 /*maxiter=1000 maxfunc=5000  can also use covtest*/;
     format region $regionformat.;
     class nPODCaseID donorgroup region;
     model  endocrine_density =region|donorgroup/solution; /*can use  ddfm = kenwardroger after solution for unbalanced data to improve performance of t and f tests*/
     /*option e3 after solution helps to describe how type 3 tests were constructed*/
     repeated  region/ subject=nPODCaseID(donorgroup)  type=hf; 
     lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;
run;
Out[136]:
SAS Output

SAS Output

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable endocrine_density
Covariance Structure Huynh-Feldt
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 1_H 2_B 3_T

Dimensions

Dimensions
Covariance Parameters 4
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 1781.81444802  
1 2 1745.34407556 0.00002130
2 1 1745.32704947 0.00000004
3 1 1745.32701730 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 914167
Var(2) nPODCaseI(donorgrou) 1946473
Var(3) nPODCaseI(donorgrou) 1484970
HF nPODCaseI(donorgrou) 671408

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 1745.3
AIC (Smaller is Better) 1753.3
AICC (Smaller is Better) 1753.7
BIC (Smaller is Better) 1760.0

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
3 36.49 <.0001

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     8709.27 325.68 35 26.74 <.0001
region   1_H 305.40 309.70 68 0.99 0.3276
region   2_B 295.43 318.50 68 0.93 0.3569
region   3_T 0 . . . .
donorgroup Autoab Pos   524.60 540.08 35 0.97 0.3380
donorgroup Ins. neg. T1D   1514.35 564.10 35 2.68 0.0110
donorgroup Ins. pos. T1D   2277.71 504.55 35 4.51 <.0001
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos 1_H -333.36 523.95 68 -0.64 0.5268
donorgroup*region Autoab Pos 2_B -409.11 518.93 68 -0.79 0.4332
donorgroup*region Autoab Pos 3_T 0 . . . .
donorgroup*region Ins. neg. T1D 1_H 373.41 536.42 68 0.70 0.4887
donorgroup*region Ins. neg. T1D 2_B 248.35 541.54 68 0.46 0.6480
donorgroup*region Ins. neg. T1D 3_T 0 . . . .
donorgroup*region Ins. pos. T1D 1_H -948.84 479.79 68 -1.98 0.0520
donorgroup*region Ins. pos. T1D 2_B 127.92 485.51 68 0.26 0.7930
donorgroup*region Ins. pos. T1D 3_T 0 . . . .
donorgroup*region No diabetes 1_H 0 . . . .
donorgroup*region No diabetes 2_B 0 . . . .
donorgroup*region No diabetes 3_T 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 1.18 0.3133
donorgroup 3 35 10.40 <.0001
donorgroup*region 6 68 1.65 0.1465

Least Squares Means

Least Squares Means
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t| Alpha Lower Upper
region   1_H 9866.63 160.53 68 61.46 <.0001 0.05 9546.29 10187
region   2_B 10076 231.92 68 43.44 <.0001 0.05 9612.87 10538
region   3_T 9788.43 201.92 68 48.48 <.0001 0.05 9385.51 10191
donorgroup Autoab Pos   9186.65 355.40 35 25.85 <.0001 0.05 8465.14 9908.16
donorgroup Ins. neg. T1D   10631 378.14 35 28.11 <.0001 0.05 9863.48 11399
donorgroup Ins. pos. T1D   10914 316.38 35 34.50 <.0001 0.05 10271 11556
donorgroup No diabetes   8909.54 268.53 35 33.18 <.0001 0.05 8364.40 9454.69
donorgroup*region Autoab Pos 1_H 9205.90 353.59 68 26.04 <.0001 0.05 8500.32 9911.49
donorgroup*region Autoab Pos 2_B 9120.19 493.26 68 18.49 <.0001 0.05 8135.89 10104
donorgroup*region Autoab Pos 3_T 9233.87 430.84 68 21.43 <.0001 0.05 8374.14 10094
donorgroup*region Ins. neg. T1D 1_H 10902 361.38 68 30.17 <.0001 0.05 10181 11624
donorgroup*region Ins. neg. T1D 2_B 10767 527.32 68 20.42 <.0001 0.05 9715.15 11820
donorgroup*region Ins. neg. T1D 3_T 10224 460.59 68 22.20 <.0001 0.05 9304.54 11143
donorgroup*region Ins. pos. T1D 1_H 10344 302.35 68 34.21 <.0001 0.05 9740.20 10947
donorgroup*region Ins. pos. T1D 2_B 11410 441.19 68 25.86 <.0001 0.05 10530 12291
donorgroup*region Ins. pos. T1D 3_T 10987 385.35 68 28.51 <.0001 0.05 10218 11756
donorgroup*region No diabetes 1_H 9014.67 255.53 68 35.28 <.0001 0.05 8504.75 9524.58
donorgroup*region No diabetes 2_B 9004.70 380.21 68 23.68 <.0001 0.05 8246.01 9763.39
donorgroup*region No diabetes 3_T 8709.27 325.68 68 26.74 <.0001 0.05 8059.38 9359.16

Differences of Least Squares Means

Differences of Least Squares Means
Effect donorgroup region _donorgroup region Estimate Standard
Error
DF t Value Pr > |t| Adjustment Adj P Alpha Lower Upper Adj Lower Adj Upper
region   1_H   2_B -209.02 194.64 68 -1.07 0.2867 Tukey-Kramer 0.5334 0.05 -597.42 179.38 -675.39 257.34
region   1_H   3_T 78.1990 193.75 68 0.40 0.6878 Tukey-Kramer 0.9142 0.05 -308.43 464.83 -386.03 542.43
region   2_B   3_T 287.22 192.91 68 1.49 0.1411 Tukey-Kramer 0.3026 0.05 -97.7148 672.16 -174.98 749.43
donorgroup Autoab Pos   Ins. neg. T1D   -1444.50 518.94 35 -2.78 0.0086 Tukey-Kramer 0.0409 0.05 -2498.01 -390.99 -2844.04 -44.9584
donorgroup Autoab Pos   Ins. pos. T1D   -1726.96 475.82 35 -3.63 0.0009 Tukey-Kramer 0.0048 0.05 -2692.93 -760.99 -3010.20 -443.72
donorgroup Autoab Pos   No diabetes   277.11 445.44 35 0.62 0.5379 Tukey-Kramer 0.9243 0.05 -627.19 1181.41 -924.21 1478.43
donorgroup Ins. neg. T1D   Ins. pos. T1D   -282.46 493.03 35 -0.57 0.5704 Tukey-Kramer 0.9395 0.05 -1283.38 718.45 -1612.13 1047.20
donorgroup Ins. neg. T1D   No diabetes   1721.61 463.79 35 3.71 0.0007 Tukey-Kramer 0.0038 0.05 780.07 2663.15 470.82 2972.40
donorgroup Ins. pos. T1D   No diabetes   2004.07 414.97 35 4.83 <.0001 Tukey-Kramer 0.0002 0.05 1161.63 2846.51 884.93 3123.21
donorgroup*region Autoab Pos 1_H Autoab Pos 2_B 85.7168 422.62 68 0.20 0.8399 Tukey-Kramer 1.0000 0.05 -757.61 929.05 -1344.59 1516.03
donorgroup*region Autoab Pos 1_H Autoab Pos 3_T -27.9634 422.62 68 -0.07 0.9474 Tukey-Kramer 1.0000 0.05 -871.29 815.37 -1458.27 1402.35
donorgroup*region Autoab Pos 1_H Ins. neg. T1D 1_H -1696.52 505.59 68 -3.36 0.0013 Tukey-Kramer 0.0540 0.05 -2705.42 -687.63 -3407.63 14.5917
donorgroup*region Autoab Pos 1_H Ins. neg. T1D 2_B -1561.50 634.90 68 -2.46 0.0165 Tukey-Kramer 0.3825 0.05 -2828.42 -294.58 -3710.23 587.23
donorgroup*region Autoab Pos 1_H Ins. neg. T1D 3_T -1017.72 580.66 68 -1.75 0.0842 Tukey-Kramer 0.8368 0.05 -2176.41 140.97 -2982.89 947.45
donorgroup*region Autoab Pos 1_H Ins. pos. T1D 1_H -1137.63 465.24 68 -2.45 0.0171 Tukey-Kramer 0.3914 0.05 -2066.00 -209.26 -2712.16 436.90
donorgroup*region Autoab Pos 1_H Ins. pos. T1D 2_B -2204.43 565.40 68 -3.90 0.0002 Tukey-Kramer 0.0111 0.05 -3332.66 -1076.19 -4117.95 -290.91
donorgroup*region Autoab Pos 1_H Ins. pos. T1D 3_T -1781.07 523.00 68 -3.41 0.0011 Tukey-Kramer 0.0472 0.05 -2824.70 -737.45 -3551.09 -11.0578
donorgroup*region Autoab Pos 1_H No diabetes 1_H 191.24 436.26 68 0.44 0.6625 Tukey-Kramer 1.0000 0.05 -679.31 1061.79 -1285.24 1667.72
donorgroup*region Autoab Pos 1_H No diabetes 2_B 201.20 519.22 68 0.39 0.6996 Tukey-Kramer 1.0000 0.05 -834.88 1237.29 -1556.02 1958.43
donorgroup*region Autoab Pos 1_H No diabetes 3_T 496.64 480.73 68 1.03 0.3052 Tukey-Kramer 0.9963 0.05 -462.64 1455.91 -1130.32 2123.59
donorgroup*region Autoab Pos 2_B Autoab Pos 3_T -113.68 409.70 68 -0.28 0.7823 Tukey-Kramer 1.0000 0.05 -931.22 703.86 -1500.25 1272.89
donorgroup*region Autoab Pos 2_B Ins. neg. T1D 1_H -1782.24 611.48 68 -2.91 0.0048 Tukey-Kramer 0.1591 0.05 -3002.42 -562.05 -3851.70 287.23
donorgroup*region Autoab Pos 2_B Ins. neg. T1D 2_B -1647.22 722.06 68 -2.28 0.0257 Tukey-Kramer 0.4994 0.05 -3088.08 -206.36 -4090.95 796.51
donorgroup*region Autoab Pos 2_B Ins. neg. T1D 3_T -1103.43 674.87 68 -1.64 0.1067 Tukey-Kramer 0.8897 0.05 -2450.11 243.25 -3387.44 1180.57
donorgroup*region Autoab Pos 2_B Ins. pos. T1D 1_H -1223.35 578.56 68 -2.11 0.0381 Tukey-Kramer 0.6145 0.05 -2377.84 -68.8583 -3181.39 734.70
donorgroup*region Autoab Pos 2_B Ins. pos. T1D 2_B -2290.14 661.78 68 -3.46 0.0009 Tukey-Kramer 0.0406 0.05 -3610.71 -969.58 -4529.86 -50.4281
donorgroup*region Autoab Pos 2_B Ins. pos. T1D 3_T -1866.79 625.94 68 -2.98 0.0040 Tukey-Kramer 0.1367 0.05 -3115.84 -617.74 -3985.21 251.64
donorgroup*region Autoab Pos 2_B No diabetes 1_H 105.52 555.52 68 0.19 0.8499 Tukey-Kramer 1.0000 0.05 -1003.01 1214.05 -1774.58 1985.62
donorgroup*region Autoab Pos 2_B No diabetes 2_B 115.49 622.79 68 0.19 0.8534 Tukey-Kramer 1.0000 0.05 -1127.27 1358.24 -1992.26 2223.24
donorgroup*region Autoab Pos 2_B No diabetes 3_T 410.92 591.08 68 0.70 0.4893 Tukey-Kramer 0.9999 0.05 -768.57 1590.41 -1589.52 2411.36
donorgroup*region Autoab Pos 3_T Ins. neg. T1D 1_H -1668.56 562.33 68 -2.97 0.0041 Tukey-Kramer 0.1415 0.05 -2790.67 -546.44 -3571.69 234.58
donorgroup*region Autoab Pos 3_T Ins. neg. T1D 2_B -1533.54 680.95 68 -2.25 0.0276 Tukey-Kramer 0.5194 0.05 -2892.35 -174.73 -3838.11 771.04
donorgroup*region Autoab Pos 3_T Ins. neg. T1D 3_T -989.75 630.68 68 -1.57 0.1212 Tukey-Kramer 0.9140 0.05 -2248.26 268.75 -3124.21 1144.71
donorgroup*region Autoab Pos 3_T Ins. pos. T1D 1_H -1109.67 526.34 68 -2.11 0.0387 Tukey-Kramer 0.6188 0.05 -2159.97 -59.3635 -2891.01 671.68
donorgroup*region Autoab Pos 3_T Ins. pos. T1D 2_B -2176.46 616.66 68 -3.53 0.0008 Tukey-Kramer 0.0335 0.05 -3406.99 -945.94 -4263.47 -89.4628
donorgroup*region Autoab Pos 3_T Ins. pos. T1D 3_T -1753.11 578.03 68 -3.03 0.0034 Tukey-Kramer 0.1216 0.05 -2906.55 -599.67 -3709.37 203.16
donorgroup*region Autoab Pos 3_T No diabetes 1_H 219.20 500.92 68 0.44 0.6631 Tukey-Kramer 1.0000 0.05 -780.36 1218.77 -1476.09 1914.49
donorgroup*region Autoab Pos 3_T No diabetes 2_B 229.17 574.61 68 0.40 0.6913 Tukey-Kramer 1.0000 0.05 -917.45 1375.79 -1715.53 2173.87
donorgroup*region Autoab Pos 3_T No diabetes 3_T 524.60 540.08 68 0.97 0.3348 Tukey-Kramer 0.9978 0.05 -553.12 1602.32 -1303.24 2352.44
donorgroup*region Ins. neg. T1D 1_H Ins. neg. T1D 2_B 135.02 437.98 68 0.31 0.7588 Tukey-Kramer 1.0000 0.05 -738.97 1009.00 -1347.28 1617.32
donorgroup*region Ins. neg. T1D 1_H Ins. neg. T1D 3_T 678.80 437.98 68 1.55 0.1258 Tukey-Kramer 0.9205 0.05 -195.18 1552.79 -803.50 2161.11
donorgroup*region Ins. neg. T1D 1_H Ins. pos. T1D 1_H 558.89 471.18 68 1.19 0.2397 Tukey-Kramer 0.9884 0.05 -381.34 1499.12 -1035.76 2153.54
donorgroup*region Ins. neg. T1D 1_H Ins. pos. T1D 2_B -507.91 570.30 68 -0.89 0.3763 Tukey-Kramer 0.9990 0.05 -1645.92 630.11 -2438.01 1422.20
donorgroup*region Ins. neg. T1D 1_H Ins. pos. T1D 3_T -84.5513 528.29 68 -0.16 0.8733 Tukey-Kramer 1.0000 0.05 -1138.74 969.64 -1872.49 1703.38
donorgroup*region Ins. neg. T1D 1_H No diabetes 1_H 1887.76 442.60 68 4.27 <.0001 Tukey-Kramer 0.0034 0.05 1004.57 2770.95 389.84 3385.67
donorgroup*region Ins. neg. T1D 1_H No diabetes 2_B 1897.72 524.55 68 3.62 0.0006 Tukey-Kramer 0.0260 0.05 851.00 2944.45 122.45 3673.00
donorgroup*region Ins. neg. T1D 1_H No diabetes 3_T 2193.16 486.48 68 4.51 <.0001 Tukey-Kramer 0.0015 0.05 1222.40 3163.92 546.72 3839.59
donorgroup*region Ins. neg. T1D 2_B Ins. neg. T1D 3_T 543.78 437.98 68 1.24 0.2187 Tukey-Kramer 0.9834 0.05 -330.20 1417.77 -938.52 2026.09
donorgroup*region Ins. neg. T1D 2_B Ins. pos. T1D 1_H 423.87 607.85 68 0.70 0.4880 Tukey-Kramer 0.9999 0.05 -789.08 1636.82 -1633.32 2481.07
donorgroup*region Ins. neg. T1D 2_B Ins. pos. T1D 2_B -642.93 687.54 68 -0.94 0.3530 Tukey-Kramer 0.9985 0.05 -2014.90 729.04 -2969.82 1683.97
donorgroup*region Ins. neg. T1D 2_B Ins. pos. T1D 3_T -219.57 653.12 68 -0.34 0.7378 Tukey-Kramer 1.0000 0.05 -1522.85 1083.71 -2429.97 1990.83
donorgroup*region Ins. neg. T1D 2_B No diabetes 1_H 1752.74 585.97 68 2.99 0.0039 Tukey-Kramer 0.1339 0.05 583.45 2922.03 -230.41 3735.89
donorgroup*region Ins. neg. T1D 2_B No diabetes 2_B 1762.71 650.10 68 2.71 0.0085 Tukey-Kramer 0.2433 0.05 465.46 3059.95 -437.46 3962.87
donorgroup*region Ins. neg. T1D 2_B No diabetes 3_T 2058.14 619.79 68 3.32 0.0014 Tukey-Kramer 0.0593 0.05 821.37 3294.91 -39.4518 4155.73
donorgroup*region Ins. neg. T1D 3_T Ins. pos. T1D 1_H -119.91 550.96 68 -0.22 0.8284 Tukey-Kramer 1.0000 0.05 -1219.33 979.51 -1984.56 1744.73
donorgroup*region Ins. neg. T1D 3_T Ins. pos. T1D 2_B -1186.71 637.80 68 -1.86 0.0671 Tukey-Kramer 0.7783 0.05 -2459.42 85.9948 -3345.25 971.83
donorgroup*region Ins. neg. T1D 3_T Ins. pos. T1D 3_T -763.35 600.53 68 -1.27 0.2080 Tukey-Kramer 0.9801 0.05 -1961.69 434.98 -2795.77 1269.06
donorgroup*region Ins. neg. T1D 3_T No diabetes 1_H 1208.96 526.72 68 2.30 0.0248 Tukey-Kramer 0.4899 0.05 157.90 2260.01 -573.67 2991.58
donorgroup*region Ins. neg. T1D 3_T No diabetes 2_B 1218.92 597.24 68 2.04 0.0451 Tukey-Kramer 0.6646 0.05 27.1462 2410.70 -802.36 3240.20
donorgroup*region Ins. neg. T1D 3_T No diabetes 3_T 1514.35 564.10 68 2.68 0.0091 Tukey-Kramer 0.2564 0.05 388.71 2640.00 -394.77 3423.47
donorgroup*region Ins. pos. T1D 1_H Ins. pos. T1D 2_B -1066.80 366.44 68 -2.91 0.0049 Tukey-Kramer 0.1604 0.05 -1798.03 -335.57 -2306.98 173.39
donorgroup*region Ins. pos. T1D 1_H Ins. pos. T1D 3_T -643.44 366.44 68 -1.76 0.0836 Tukey-Kramer 0.8352 0.05 -1374.67 87.7867 -1883.63 596.74
donorgroup*region Ins. pos. T1D 1_H No diabetes 1_H 1328.87 395.87 68 3.36 0.0013 Tukey-Kramer 0.0538 0.05 538.92 2118.82 -10.9074 2668.64
donorgroup*region Ins. pos. T1D 1_H No diabetes 2_B 1338.83 485.77 68 2.76 0.0075 Tukey-Kramer 0.2226 0.05 369.49 2308.18 -305.20 2982.86
donorgroup*region Ins. pos. T1D 1_H No diabetes 3_T 1634.27 444.39 68 3.68 0.0005 Tukey-Kramer 0.0218 0.05 747.49 2521.04 130.27 3138.26
donorgroup*region Ins. pos. T1D 2_B Ins. pos. T1D 3_T 423.36 366.44 68 1.16 0.2520 Tukey-Kramer 0.9906 0.05 -307.87 1154.58 -816.83 1663.54
donorgroup*region Ins. pos. T1D 2_B No diabetes 1_H 2395.67 509.85 68 4.70 <.0001 Tukey-Kramer 0.0008 0.05 1378.28 3413.05 670.15 4121.18
donorgroup*region Ins. pos. T1D 2_B No diabetes 2_B 2405.63 582.41 68 4.13 0.0001 Tukey-Kramer 0.0053 0.05 1243.44 3567.82 434.53 4376.73
donorgroup*region Ins. pos. T1D 2_B No diabetes 3_T 2701.06 548.38 68 4.93 <.0001 Tukey-Kramer 0.0003 0.05 1606.80 3795.33 845.16 4556.97
donorgroup*region Ins. pos. T1D 3_T No diabetes 1_H 1972.31 462.38 68 4.27 <.0001 Tukey-Kramer 0.0034 0.05 1049.65 2894.97 407.45 3537.17
donorgroup*region Ins. pos. T1D 3_T No diabetes 2_B 1982.28 541.35 68 3.66 0.0005 Tukey-Kramer 0.0229 0.05 902.04 3062.51 150.16 3814.39
donorgroup*region Ins. pos. T1D 3_T No diabetes 3_T 2277.71 504.55 68 4.51 <.0001 Tukey-Kramer 0.0015 0.05 1270.90 3284.51 570.14 3985.28
donorgroup*region No diabetes 1_H No diabetes 2_B 9.9657 318.50 68 0.03 0.9751 Tukey-Kramer 1.0000 0.05 -625.58 645.51 -1067.94 1087.87
donorgroup*region No diabetes 1_H No diabetes 3_T 305.40 309.70 68 0.99 0.3276 Tukey-Kramer 0.9975 0.05 -312.60 923.40 -742.75 1353.54
donorgroup*region No diabetes 2_B No diabetes 3_T 295.43 318.50 68 0.93 0.3569 Tukey-Kramer 0.9986 0.05 -340.12 930.98 -782.47 1373.34
In [137]:
%explore('islets: Avg Cell Area (cell size'n);
Out[137]:
SAS Output

SAS Output

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable islets: Avg Cell Area (cell size
Covariance Structure Variance Components
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method Parameter
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 1
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 641.13381379  
1 1 641.13381379 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
region nPODCaseI(donorgrou) 22.8183

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 641.1
AIC (Smaller is Better) 643.1
AICC (Smaller is Better) 643.2
BIC (Smaller is Better) 644.8

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
0 0.00 1.0000

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     72.5192 1.2767 35 56.80 <.0001
region   PB -1.3821 1.8399 68 -0.75 0.4551
region   PH -1.0652 1.8055 68 -0.59 0.5571
region   PT 0 . . . .
donorgroup Autoab Pos   -2.9760 2.1171 35 -1.41 0.1686
donorgroup Ins. neg. T1D   -5.5950 2.2113 35 -2.53 0.0161
donorgroup Ins. pos. T1D   -7.9458 1.9778 35 -4.02 0.0003
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB 2.8061 3.0149 68 0.93 0.3553
donorgroup*region Autoab Pos PH 2.1251 3.0613 68 0.69 0.4899
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB -1.8326 3.1472 68 -0.58 0.5623
donorgroup*region Ins. neg. T1D PH -1.0812 3.1272 68 -0.35 0.7306
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB -0.02612 2.8194 68 -0.01 0.9926
donorgroup*region Ins. pos. T1D PH 1.2687 2.7970 68 0.45 0.6516
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 0.52 0.5947
donorgroup 3 35 18.90 <.0001
donorgroup*region 6 68 0.37 0.8951

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable islets: Avg Cell Area (cell size
Covariance Structure Compound Symmetry
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method Profile
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 2
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 641.13381379  
1 2 593.64364866 0.00001632
2 1 593.64028905 0.00000001
3 1 593.64028651 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
CS nPODCaseI(donorgrou) 15.8866
Residual   7.2921

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 593.6
AIC (Smaller is Better) 597.6
AICC (Smaller is Better) 597.8
BIC (Smaller is Better) 601.0

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
1 47.49 <.0001

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     72.5192 1.2867 35 56.36 <.0001
region   PB -0.8088 1.0479 68 -0.77 0.4429
region   PH -1.0652 1.0207 68 -1.04 0.3003
region   PT 0 . . . .
donorgroup Autoab Pos   -2.9760 2.1338 35 -1.39 0.1719
donorgroup Ins. neg. T1D   -5.5950 2.2286 35 -2.51 0.0168
donorgroup Ins. pos. T1D   -7.9458 1.9934 35 -3.99 0.0003
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB 2.2328 1.7091 68 1.31 0.1958
donorgroup*region Autoab Pos PH 1.8882 1.7458 68 1.08 0.2833
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB -2.4060 1.7837 68 -1.35 0.1819
donorgroup*region Ins. neg. T1D PH -1.0812 1.7678 68 -0.61 0.5428
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB -0.5994 1.5989 68 -0.37 0.7089
donorgroup*region Ins. pos. T1D PH 1.2687 1.5812 68 0.80 0.4251
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 1.25 0.2940
donorgroup 3 35 8.22 0.0003
donorgroup*region 6 68 1.20 0.3183

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable islets: Avg Cell Area (cell size
Covariance Structure Unstructured
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 6
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 641.13381379  
1 2 588.41008751 0.00203612
2 1 587.94780956 0.00013307
3 1 587.91997328 0.00000083
4 1 587.91980645 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
UN(1,1) nPODCaseI(donorgrou) 22.9615
UN(2,1) nPODCaseI(donorgrou) 13.7570
UN(2,2) nPODCaseI(donorgrou) 16.6125
UN(3,1) nPODCaseI(donorgrou) 18.3557
UN(3,2) nPODCaseI(donorgrou) 15.3892
UN(3,3) nPODCaseI(donorgrou) 29.7269

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 587.9
AIC (Smaller is Better) 599.9
AICC (Smaller is Better) 600.8
BIC (Smaller is Better) 609.9

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
5 53.21 <.0001

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     72.5192 1.4572 35 49.77 <.0001
region   PB -0.8247 1.0925 35 -0.75 0.4554
region   PH -1.0652 1.0543 35 -1.01 0.3192
region   PT 0 . . . .
donorgroup Autoab Pos   -2.9760 2.4164 35 -1.23 0.2263
donorgroup Ins. neg. T1D   -5.5950 2.5239 35 -2.22 0.0332
donorgroup Ins. pos. T1D   -7.9458 2.2574 35 -3.52 0.0012
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB 2.2486 1.7863 35 1.26 0.2164
donorgroup*region Autoab Pos PH 1.9331 1.7842 35 1.08 0.2860
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB -2.3901 1.8644 35 -1.28 0.2083
donorgroup*region Ins. neg. T1D PH -1.0812 1.8261 35 -0.59 0.5576
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB -0.5836 1.6707 35 -0.35 0.7290
donorgroup*region Ins. pos. T1D PH 1.2687 1.6333 35 0.78 0.4425
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 35 1.15 0.3269
donorgroup 3 35 8.25 0.0003
donorgroup*region 6 35 1.14 0.3596

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable islets: Avg Cell Area (cell size
Covariance Structure Unstructured using Correlations
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 6
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 641.13381379  
1 2 588.45963778 0.00219427
2 1 587.95806619 0.00017899
3 1 587.92017282 0.00000183
4 1 587.91980648 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 22.9618
Var(2) nPODCaseI(donorgrou) 16.6126
Var(3) nPODCaseI(donorgrou) 29.7272
Corr(2,1) nPODCaseI(donorgrou) 0.7044
Corr(3,1) nPODCaseI(donorgrou) 0.7026
Corr(3,2) nPODCaseI(donorgrou) 0.6925

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 587.9
AIC (Smaller is Better) 599.9
AICC (Smaller is Better) 600.8
BIC (Smaller is Better) 609.9

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
5 53.21 <.0001

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     72.5192 1.4572 35 49.77 <.0001
region   PB -0.8246 1.0925 35 -0.75 0.4554
region   PH -1.0652 1.0543 35 -1.01 0.3192
region   PT 0 . . . .
donorgroup Autoab Pos   -2.9760 2.4165 35 -1.23 0.2263
donorgroup Ins. neg. T1D   -5.5950 2.5239 35 -2.22 0.0332
donorgroup Ins. pos. T1D   -7.9458 2.2575 35 -3.52 0.0012
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB 2.2486 1.7862 35 1.26 0.2164
donorgroup*region Autoab Pos PH 1.9331 1.7842 35 1.08 0.2860
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB -2.3901 1.8644 35 -1.28 0.2083
donorgroup*region Ins. neg. T1D PH -1.0812 1.8261 35 -0.59 0.5576
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB -0.5836 1.6707 35 -0.35 0.7290
donorgroup*region Ins. pos. T1D PH 1.2687 1.6333 35 0.78 0.4425
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 35 1.15 0.3268
donorgroup 3 35 8.25 0.0003
donorgroup*region 6 35 1.14 0.3596

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable islets: Avg Cell Area (cell size
Covariance Structure Banded
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 6
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 45 641.13381379  
1 44 2566.28322898 0.46214266
2 44 2566.28322898 0.46214266

Convergence Status

WARNING: Stopped because of too many likelihood evaluations.

Covariance Parameter Values At Last Iteration

Covariance Parameter Values At Last Iteration
Cov Parm Subject Estimate
UN(1,1) nPODCaseI(donorgrou) 1.0000
UN(2,1) nPODCaseI(donorgrou) 0
UN(2,2) nPODCaseI(donorgrou) 1.0000
UN(3,1) nPODCaseI(donorgrou) 0
UN(3,2) nPODCaseI(donorgrou) 0
UN(3,3) nPODCaseI(donorgrou) 1.0000

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable islets: Avg Cell Area (cell size
Covariance Structure Heterogeneous Compound Symmetry
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 4
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 641.13381379  
1 2 587.94511776 0.00002057
2 1 587.94096266 0.00000001
3 1 587.94096064 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 22.8560
Var(2) nPODCaseI(donorgrou) 16.6296
Var(3) nPODCaseI(donorgrou) 29.7950
CSH nPODCaseI(donorgrou) 0.6995

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 587.9
AIC (Smaller is Better) 595.9
AICC (Smaller is Better) 596.3
BIC (Smaller is Better) 602.6

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
3 53.19 <.0001

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     72.5192 1.4588 35 49.71 <.0001
region   PB -0.8304 1.0982 68 -0.76 0.4522
region   PH -1.0652 1.0448 68 -1.02 0.3115
region   PT 0 . . . .
donorgroup Autoab Pos   -2.9760 2.4192 35 -1.23 0.2268
donorgroup Ins. neg. T1D   -5.5950 2.5268 35 -2.21 0.0334
donorgroup Ins. pos. T1D   -7.9458 2.2600 35 -3.52 0.0012
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB 2.2543 1.7955 68 1.26 0.2136
donorgroup*region Autoab Pos PH 1.9330 1.7685 68 1.09 0.2783
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB -2.3844 1.8740 68 -1.27 0.2076
donorgroup*region Ins. neg. T1D PH -1.0812 1.8096 68 -0.60 0.5522
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB -0.5778 1.6793 68 -0.34 0.7318
donorgroup*region Ins. pos. T1D PH 1.2687 1.6186 68 0.78 0.4358
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 1.14 0.3249
donorgroup 3 35 8.25 0.0003
donorgroup*region 6 68 1.13 0.3535

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable islets: Avg Cell Area (cell size
Covariance Structure Huynh-Feldt
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 4
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 641.13381379  
1 2 589.02533611 0.00086131
2 1 588.83843111 0.00001943
3 1 588.83448006 0.00000002
4 1 588.83447700 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 24.8410
Var(2) nPODCaseI(donorgrou) 16.7285
Var(3) nPODCaseI(donorgrou) 28.2383
HF nPODCaseI(donorgrou) 7.2518

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 588.8
AIC (Smaller is Better) 596.8
AICC (Smaller is Better) 597.2
BIC (Smaller is Better) 603.5

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
3 52.30 <.0001

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     72.5192 1.4202 35 51.06 <.0001
region   PB -0.7404 1.0458 68 -0.71 0.4814
region   PH -1.0652 1.0178 68 -1.05 0.2990
region   PT 0 . . . .
donorgroup Autoab Pos   -2.9760 2.3552 35 -1.26 0.2147
donorgroup Ins. neg. T1D   -5.5949 2.4599 35 -2.27 0.0292
donorgroup Ins. pos. T1D   -7.9458 2.2002 35 -3.61 0.0009
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB 2.1644 1.7049 68 1.27 0.2086
donorgroup*region Autoab Pos PH 1.9438 1.7280 68 1.12 0.2646
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB -2.4743 1.7792 68 -1.39 0.1689
donorgroup*region Ins. neg. T1D PH -1.0812 1.7629 68 -0.61 0.5417
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB -0.6678 1.5950 68 -0.42 0.6768
donorgroup*region Ins. pos. T1D PH 1.2687 1.5768 68 0.80 0.4238
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 1.21 0.3045
donorgroup 3 35 8.22 0.0003
donorgroup*region 6 68 1.22 0.3078

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable islets: Avg Cell Area (cell size
Covariance Structure Heterogeneous Autoregressive
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 4
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 641.13381379  
1 2 593.54690404 0.00020163
2 1 593.50427192 0.00000110
3 1 593.50404810 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 21.7768
Var(2) nPODCaseI(donorgrou) 16.5946
Var(3) nPODCaseI(donorgrou) 29.7772
ARH(1) nPODCaseI(donorgrou) 0.6953

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 593.5
AIC (Smaller is Better) 601.5
AICC (Smaller is Better) 601.9
BIC (Smaller is Better) 608.2

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
3 47.63 <.0001

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     72.5192 1.4584 35 49.73 <.0001
region   PB -1.0983 1.4090 68 -0.78 0.4384
region   PH -1.0652 1.0508 68 -1.01 0.3143
region   PT 0 . . . .
donorgroup Autoab Pos   -2.9760 2.4185 35 -1.23 0.2267
donorgroup Ins. neg. T1D   -5.5949 2.5260 35 -2.21 0.0334
donorgroup Ins. pos. T1D   -7.9458 2.2593 35 -3.52 0.0012
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB 2.5223 2.3134 68 1.09 0.2794
donorgroup*region Autoab Pos PH 1.9036 1.7719 68 1.07 0.2865
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB -2.1164 2.4151 68 -0.88 0.3839
donorgroup*region Ins. neg. T1D PH -1.0812 1.8200 68 -0.59 0.5544
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB -0.3099 2.1630 68 -0.14 0.8865
donorgroup*region Ins. pos. T1D PH 1.2687 1.6279 68 0.78 0.4385
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 0.79 0.4597
donorgroup 3 35 8.84 0.0002
donorgroup*region 6 68 0.84 0.5446

The SAS System

The PRINT Procedure

Data Set WORK.ALL

Description arh1 cs csh hf un unr vc
-2 Res Log Likelihood 593.5 593.6 587.9 588.8 587.9 587.9 641.1
AIC (Smaller is Better) 601.5 597.6 595.9 596.8 599.9 599.9 643.1
AICC (Smaller is Better) 601.9 597.8 596.3 597.2 600.8 600.8 643.2
BIC (Smaller is Better) 608.2 601.0 602.6 603.5 609.9 609.9 644.8

The SAS System

The PRINT Procedure

Data Set WORK.STATUS

Obs Reason Status pdG pdH covar
1 Convergence criteria met. 0 1 1 arh(1)
2 Convergence criteria met. 0 1 1 cs
3 Convergence criteria met. 0 1 1 csh
4 Convergence criteria met. 0 1 1 hf
5 Convergence criteria met. 0 1 1 un
6 WARNING: Stopped because of too many likelihood evaluations. 1 1 1 un1
7 Convergence criteria met. 0 1 1 unr
8 Convergence criteria met. 0 1 1 vc
In [138]:
PROC mixed data=cell3 /*maxiter=1000 maxfunc=5000  can also use covtest*/;
     format region $regionformat.;
     class nPODCaseID donorgroup region;
     model  'islets: Avg Cell Area (cell size'n =region|donorgroup/solution; /*can use  ddfm = kenwardroger after solution for unbalanced data to improve performance of t and f tests*/
     /*option e3 after solution helps to describe how type 3 tests were constructed*/
     repeated  region/ subject=nPODCaseID(donorgroup)  type=csh; 
     lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;
run;
Out[138]:
SAS Output

SAS Output

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable islets: Avg Cell Area (cell size
Covariance Structure Heterogeneous Compound Symmetry
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 1_H 2_B 3_T

Dimensions

Dimensions
Covariance Parameters 4
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 641.13381379  
1 2 587.94511776 0.00002057
2 1 587.94096266 0.00000001
3 1 587.94096064 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 16.6296
Var(2) nPODCaseI(donorgrou) 22.8560
Var(3) nPODCaseI(donorgrou) 29.7950
CSH nPODCaseI(donorgrou) 0.6995

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 587.9
AIC (Smaller is Better) 595.9
AICC (Smaller is Better) 596.3
BIC (Smaller is Better) 602.6

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
3 53.19 <.0001

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     72.5192 1.4588 35 49.71 <.0001
region   1_H -1.0652 1.0448 68 -1.02 0.3115
region   2_B -0.8304 1.0982 68 -0.76 0.4522
region   3_T 0 . . . .
donorgroup Autoab Pos   -2.9760 2.4192 35 -1.23 0.2268
donorgroup Ins. neg. T1D   -5.5949 2.5268 35 -2.21 0.0334
donorgroup Ins. pos. T1D   -7.9458 2.2600 35 -3.52 0.0012
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos 1_H 1.9330 1.7685 68 1.09 0.2783
donorgroup*region Autoab Pos 2_B 2.2543 1.7955 68 1.26 0.2136
donorgroup*region Autoab Pos 3_T 0 . . . .
donorgroup*region Ins. neg. T1D 1_H -1.0812 1.8096 68 -0.60 0.5522
donorgroup*region Ins. neg. T1D 2_B -2.3844 1.8740 68 -1.27 0.2076
donorgroup*region Ins. neg. T1D 3_T 0 . . . .
donorgroup*region Ins. pos. T1D 1_H 1.2687 1.6186 68 0.78 0.4358
donorgroup*region Ins. pos. T1D 2_B -0.5778 1.6793 68 -0.34 0.7318
donorgroup*region Ins. pos. T1D 3_T 0 . . . .
donorgroup*region No diabetes 1_H 0 . . . .
donorgroup*region No diabetes 2_B 0 . . . .
donorgroup*region No diabetes 3_T 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 1.14 0.3249
donorgroup 3 35 8.25 0.0003
donorgroup*region 6 68 1.13 0.3535

Least Squares Means

Least Squares Means
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t| Alpha Lower Upper
region   1_H 67.8549 0.6815 68 99.57 <.0001 0.05 66.4950 69.2148
region   2_B 67.3827 0.7943 68 84.84 <.0001 0.05 65.7977 68.9676
region   3_T 68.3900 0.9045 68 75.61 <.0001 0.05 66.5852 70.1948
donorgroup Autoab Pos   70.3071 1.5148 35 46.41 <.0001 0.05 67.2318 73.3824
donorgroup Ins. neg. T1D   65.1372 1.6145 35 40.35 <.0001 0.05 61.8597 68.4148
donorgroup Ins. pos. T1D   64.1718 1.3508 35 47.51 <.0001 0.05 61.4296 66.9140
donorgroup No diabetes   71.8874 1.1442 35 62.83 <.0001 0.05 69.5645 74.2102
donorgroup*region Autoab Pos 1_H 70.4110 1.4848 68 47.42 <.0001 0.05 67.4481 73.3738
donorgroup*region Autoab Pos 2_B 70.9672 1.6903 68 41.99 <.0001 0.05 67.5943 74.3400
donorgroup*region Autoab Pos 3_T 69.5432 1.9299 68 36.04 <.0001 0.05 65.6922 73.3942
donorgroup*region Ins. neg. T1D 1_H 64.7779 1.5413 68 42.03 <.0001 0.05 61.7022 67.8535
donorgroup*region Ins. neg. T1D 2_B 63.7095 1.8070 68 35.26 <.0001 0.05 60.1038 67.3153
donorgroup*region Ins. neg. T1D 3_T 66.9243 2.0631 68 32.44 <.0001 0.05 62.8074 71.0412
donorgroup*region Ins. pos. T1D 1_H 64.7769 1.2896 68 50.23 <.0001 0.05 62.2036 67.3502
donorgroup*region Ins. pos. T1D 2_B 63.1652 1.5118 68 41.78 <.0001 0.05 60.1484 66.1819
donorgroup*region Ins. pos. T1D 3_T 64.5734 1.7261 68 37.41 <.0001 0.05 61.1290 68.0178
donorgroup*region No diabetes 1_H 71.4540 1.0899 68 65.56 <.0001 0.05 69.2792 73.6288
donorgroup*region No diabetes 2_B 71.6888 1.2984 68 55.21 <.0001 0.05 69.0979 74.2797
donorgroup*region No diabetes 3_T 72.5192 1.4588 68 49.71 <.0001 0.05 69.6082 75.4303

Differences of Least Squares Means

Differences of Least Squares Means
Effect donorgroup region _donorgroup region Estimate Standard
Error
DF t Value Pr > |t| Adjustment Adj P Alpha Lower Upper Adj Lower Adj Upper
region   1_H   2_B 0.4723 0.5886 68 0.80 0.4251 Tukey-Kramer 0.7028 0.05 -0.7022 1.6467 -0.9379 1.8825
region   1_H   3_T -0.5351 0.6538 68 -0.82 0.4159 Tukey-Kramer 0.6929 0.05 -1.8397 0.7695 -2.1016 1.0314
region   2_B   3_T -1.0074 0.6682 68 -1.51 0.1363 Tukey-Kramer 0.2938 0.05 -2.3407 0.3260 -2.6083 0.5936
donorgroup Autoab Pos   Ins. neg. T1D   5.1699 2.2139 35 2.34 0.0254 Tukey-Kramer 0.1094 0.05 0.6755 9.6643 -0.8007 11.1405
donorgroup Autoab Pos   Ins. pos. T1D   6.1353 2.0296 35 3.02 0.0047 Tukey-Kramer 0.0230 0.05 2.0150 10.2556 0.6617 11.6089
donorgroup Autoab Pos   No diabetes   -1.5803 1.8984 35 -0.83 0.4108 Tukey-Kramer 0.8387 0.05 -5.4342 2.2737 -6.7000 3.5395
donorgroup Ins. neg. T1D   Ins. pos. T1D   0.9654 2.1050 35 0.46 0.6493 Tukey-Kramer 0.9675 0.05 -3.3080 5.2388 -4.7116 6.6424
donorgroup Ins. neg. T1D   No diabetes   -6.7501 1.9788 35 -3.41 0.0016 Tukey-Kramer 0.0085 0.05 -10.7673 -2.7329 -12.0868 -1.4135
donorgroup Ins. pos. T1D   No diabetes   -7.7155 1.7702 35 -4.36 0.0001 Tukey-Kramer 0.0006 0.05 -11.3093 -4.1218 -12.4897 -2.9414
donorgroup*region Autoab Pos 1_H Autoab Pos 2_B -0.5562 1.2853 68 -0.43 0.6666 Tukey-Kramer 1.0000 0.05 -3.1210 2.0086 -4.9062 3.7938
donorgroup*region Autoab Pos 1_H Autoab Pos 3_T 0.8678 1.4269 68 0.61 0.5451 Tukey-Kramer 1.0000 0.05 -1.9797 3.7152 -3.9615 5.6970
donorgroup*region Autoab Pos 1_H Ins. neg. T1D 1_H 5.6331 2.1402 68 2.63 0.0105 Tukey-Kramer 0.2831 0.05 1.3625 9.9037 -1.6100 12.8762
donorgroup*region Autoab Pos 1_H Ins. neg. T1D 2_B 6.7014 2.3388 68 2.87 0.0055 Tukey-Kramer 0.1772 0.05 2.0345 11.3683 -1.2138 14.6166
donorgroup*region Autoab Pos 1_H Ins. neg. T1D 3_T 3.4867 2.5419 68 1.37 0.1747 Tukey-Kramer 0.9651 0.05 -1.5855 8.5589 -5.1159 12.0893
donorgroup*region Autoab Pos 1_H Ins. pos. T1D 1_H 5.6341 1.9666 68 2.86 0.0055 Tukey-Kramer 0.1774 0.05 1.7097 9.5584 -1.0217 12.2898
donorgroup*region Autoab Pos 1_H Ins. pos. T1D 2_B 7.2458 2.1190 68 3.42 0.0011 Tukey-Kramer 0.0455 0.05 3.0174 11.4742 0.07426 14.4173
donorgroup*region Autoab Pos 1_H Ins. pos. T1D 3_T 5.8376 2.2769 68 2.56 0.0126 Tukey-Kramer 0.3204 0.05 1.2941 10.3810 -1.8682 13.5433
donorgroup*region Autoab Pos 1_H No diabetes 1_H -1.0431 1.8419 68 -0.57 0.5731 Tukey-Kramer 1.0000 0.05 -4.7184 2.6323 -7.2766 5.1905
donorgroup*region Autoab Pos 1_H No diabetes 2_B -1.2779 1.9724 68 -0.65 0.5192 Tukey-Kramer 1.0000 0.05 -5.2138 2.6580 -7.9533 5.3975
donorgroup*region Autoab Pos 1_H No diabetes 3_T -2.1083 2.0816 68 -1.01 0.3147 Tukey-Kramer 0.9969 0.05 -6.2620 2.0454 -9.1530 4.9365
donorgroup*region Autoab Pos 2_B Autoab Pos 3_T 1.4240 1.4204 68 1.00 0.3197 Tukey-Kramer 0.9972 0.05 -1.4104 4.2583 -3.3832 6.2311
donorgroup*region Autoab Pos 2_B Ins. neg. T1D 1_H 6.1893 2.2875 68 2.71 0.0086 Tukey-Kramer 0.2460 0.05 1.6247 10.7539 -1.5524 13.9310
donorgroup*region Autoab Pos 2_B Ins. neg. T1D 2_B 7.2576 2.4743 68 2.93 0.0046 Tukey-Kramer 0.1527 0.05 2.3202 12.1950 -1.1163 15.6315
donorgroup*region Autoab Pos 2_B Ins. neg. T1D 3_T 4.0429 2.6671 68 1.52 0.1342 Tukey-Kramer 0.9310 0.05 -1.2793 9.3650 -4.9836 13.0693
donorgroup*region Autoab Pos 2_B Ins. pos. T1D 1_H 6.1903 2.1260 68 2.91 0.0049 Tukey-Kramer 0.1602 0.05 1.9479 10.4327 -1.0050 13.3855
donorgroup*region Autoab Pos 2_B Ins. pos. T1D 2_B 7.8020 2.2677 68 3.44 0.0010 Tukey-Kramer 0.0429 0.05 3.2768 12.3272 0.1272 15.4768
donorgroup*region Autoab Pos 2_B Ins. pos. T1D 3_T 6.3938 2.4159 68 2.65 0.0101 Tukey-Kramer 0.2756 0.05 1.5729 11.2146 -1.7825 14.5700
donorgroup*region Autoab Pos 2_B No diabetes 1_H -0.4869 2.0112 68 -0.24 0.8094 Tukey-Kramer 1.0000 0.05 -4.5001 3.5264 -7.2934 6.3197
donorgroup*region Autoab Pos 2_B No diabetes 2_B -0.7217 2.1314 68 -0.34 0.7360 Tukey-Kramer 1.0000 0.05 -4.9748 3.5314 -7.9351 6.4917
donorgroup*region Autoab Pos 2_B No diabetes 3_T -1.5521 2.2328 68 -0.70 0.4893 Tukey-Kramer 0.9999 0.05 -6.0075 2.9033 -9.1086 6.0044
donorgroup*region Autoab Pos 3_T Ins. neg. T1D 1_H 4.7653 2.4698 68 1.93 0.0579 Tukey-Kramer 0.7369 0.05 -0.1631 9.6938 -3.5934 13.1241
donorgroup*region Autoab Pos 3_T Ins. neg. T1D 2_B 5.8337 2.6438 68 2.21 0.0307 Tukey-Kramer 0.5508 0.05 0.5581 11.1092 -3.1138 14.7812
donorgroup*region Autoab Pos 3_T Ins. neg. T1D 3_T 2.6189 2.8250 68 0.93 0.3572 Tukey-Kramer 0.9986 0.05 -3.0183 8.2562 -6.9420 12.1799
donorgroup*region Autoab Pos 3_T Ins. pos. T1D 1_H 4.7663 2.3211 68 2.05 0.0439 Tukey-Kramer 0.6561 0.05 0.1347 9.3979 -3.0890 12.6216
donorgroup*region Autoab Pos 3_T Ins. pos. T1D 2_B 6.3780 2.4515 68 2.60 0.0114 Tukey-Kramer 0.2994 0.05 1.4861 11.2700 -1.9188 14.6749
donorgroup*region Autoab Pos 3_T Ins. pos. T1D 3_T 4.9698 2.5892 68 1.92 0.0591 Tukey-Kramer 0.7431 0.05 -0.1968 10.1364 -3.7929 13.7326
donorgroup*region Autoab Pos 3_T No diabetes 1_H -1.9108 2.2163 68 -0.86 0.3916 Tukey-Kramer 0.9993 0.05 -6.3335 2.5118 -9.4117 5.5901
donorgroup*region Autoab Pos 3_T No diabetes 2_B -2.1456 2.3260 68 -0.92 0.3595 Tukey-Kramer 0.9986 0.05 -6.7871 2.4958 -10.0176 5.7264
donorgroup*region Autoab Pos 3_T No diabetes 3_T -2.9760 2.4192 68 -1.23 0.2229 Tukey-Kramer 0.9845 0.05 -7.8035 1.8514 -11.1635 5.2115
donorgroup*region Ins. neg. T1D 1_H Ins. neg. T1D 2_B 1.0683 1.3207 68 0.81 0.4214 Tukey-Kramer 0.9996 0.05 -1.5670 3.7037 -3.4013 5.5379
donorgroup*region Ins. neg. T1D 1_H Ins. neg. T1D 3_T -2.1464 1.4775 68 -1.45 0.1509 Tukey-Kramer 0.9479 0.05 -5.0948 0.8019 -7.1469 2.8541
donorgroup*region Ins. neg. T1D 1_H Ins. pos. T1D 1_H 0.000972 2.0096 68 0.00 0.9996 Tukey-Kramer 1.0000 0.05 -4.0092 4.0111 -6.8003 6.8023
donorgroup*region Ins. neg. T1D 1_H Ins. pos. T1D 2_B 1.6127 2.1590 68 0.75 0.4577 Tukey-Kramer 0.9998 0.05 -2.6955 5.9209 -5.6941 8.9195
donorgroup*region Ins. neg. T1D 1_H Ins. pos. T1D 3_T 0.2045 2.3141 68 0.09 0.9299 Tukey-Kramer 1.0000 0.05 -4.4133 4.8222 -7.6274 8.0363
donorgroup*region Ins. neg. T1D 1_H No diabetes 1_H -6.6762 1.8877 68 -3.54 0.0007 Tukey-Kramer 0.0328 0.05 -10.4430 -2.9093 -13.0649 -0.2874
donorgroup*region Ins. neg. T1D 1_H No diabetes 2_B -6.9110 2.0153 68 -3.43 0.0010 Tukey-Kramer 0.0443 0.05 -10.9325 -2.8895 -13.7315 -0.09042
donorgroup*region Ins. neg. T1D 1_H No diabetes 3_T -7.7414 2.1222 68 -3.65 0.0005 Tukey-Kramer 0.0238 0.05 -11.9762 -3.5065 -14.9238 -0.5590
donorgroup*region Ins. neg. T1D 2_B Ins. neg. T1D 3_T -3.2148 1.5185 68 -2.12 0.0379 Tukey-Kramer 0.6127 0.05 -6.2448 -0.1847 -8.3538 1.9243
donorgroup*region Ins. neg. T1D 2_B Ins. pos. T1D 1_H -1.0674 2.2199 68 -0.48 0.6322 Tukey-Kramer 1.0000 0.05 -5.4972 3.3624 -8.5804 6.4457
donorgroup*region Ins. neg. T1D 2_B Ins. pos. T1D 2_B 0.5444 2.3560 68 0.23 0.8180 Tukey-Kramer 1.0000 0.05 -4.1570 5.2457 -7.4292 8.5179
donorgroup*region Ins. neg. T1D 2_B Ins. pos. T1D 3_T -0.8639 2.4989 68 -0.35 0.7306 Tukey-Kramer 1.0000 0.05 -5.8504 4.1227 -9.3212 7.5934
donorgroup*region Ins. neg. T1D 2_B No diabetes 1_H -7.7445 2.1102 68 -3.67 0.0005 Tukey-Kramer 0.0223 0.05 -11.9553 -3.5336 -14.8862 -0.6028
donorgroup*region Ins. neg. T1D 2_B No diabetes 2_B -7.9793 2.2251 68 -3.59 0.0006 Tukey-Kramer 0.0285 0.05 -12.4194 -3.5392 -15.5098 -0.4488
donorgroup*region Ins. neg. T1D 2_B No diabetes 3_T -8.8097 2.3224 68 -3.79 0.0003 Tukey-Kramer 0.0154 0.05 -13.4439 -4.1755 -16.6694 -0.9500
donorgroup*region Ins. neg. T1D 3_T Ins. pos. T1D 1_H 2.1474 2.4330 68 0.88 0.3806 Tukey-Kramer 0.9991 0.05 -2.7075 7.0023 -6.0867 10.3815
donorgroup*region Ins. neg. T1D 3_T Ins. pos. T1D 2_B 3.7591 2.5577 68 1.47 0.1463 Tukey-Kramer 0.9437 0.05 -1.3448 8.8630 -4.8972 12.4155
donorgroup*region Ins. neg. T1D 3_T Ins. pos. T1D 3_T 2.3509 2.6900 68 0.87 0.3852 Tukey-Kramer 0.9992 0.05 -3.0169 7.7186 -6.7529 11.4547
donorgroup*region Ins. neg. T1D 3_T No diabetes 1_H -4.5297 2.3333 68 -1.94 0.0564 Tukey-Kramer 0.7295 0.05 -9.1857 0.1263 -12.4264 3.3670
donorgroup*region Ins. neg. T1D 3_T No diabetes 2_B -4.7646 2.4377 68 -1.95 0.0547 Tukey-Kramer 0.7211 0.05 -9.6289 0.09975 -13.0145 3.4854
donorgroup*region Ins. neg. T1D 3_T No diabetes 3_T -5.5949 2.5268 68 -2.21 0.0302 Tukey-Kramer 0.5455 0.05 -10.6371 -0.5528 -14.1465 2.9566
donorgroup*region Ins. pos. T1D 1_H Ins. pos. T1D 2_B 1.6117 1.1049 68 1.46 0.1493 Tukey-Kramer 0.9465 0.05 -0.5932 3.8166 -2.1278 5.3513
donorgroup*region Ins. pos. T1D 1_H Ins. pos. T1D 3_T 0.2035 1.2362 68 0.16 0.8697 Tukey-Kramer 1.0000 0.05 -2.2633 2.6703 -3.9802 4.3872
donorgroup*region Ins. pos. T1D 1_H No diabetes 1_H -6.6771 1.6884 68 -3.95 0.0002 Tukey-Kramer 0.0094 0.05 -10.0463 -3.3079 -12.3914 -0.9629
donorgroup*region Ins. pos. T1D 1_H No diabetes 2_B -6.9120 1.8300 68 -3.78 0.0003 Tukey-Kramer 0.0162 0.05 -10.5636 -3.2603 -13.1052 -0.7187
donorgroup*region Ins. pos. T1D 1_H No diabetes 3_T -7.7424 1.9471 68 -3.98 0.0002 Tukey-Kramer 0.0087 0.05 -11.6277 -3.8570 -14.3320 -1.1527
donorgroup*region Ins. pos. T1D 2_B Ins. pos. T1D 3_T -1.4082 1.2704 68 -1.11 0.2716 Tukey-Kramer 0.9933 0.05 -3.9434 1.1269 -5.7079 2.8914
donorgroup*region Ins. pos. T1D 2_B No diabetes 1_H -8.2889 1.8637 68 -4.45 <.0001 Tukey-Kramer 0.0018 0.05 -12.0078 -4.5699 -14.5963 -1.9814
donorgroup*region Ins. pos. T1D 2_B No diabetes 2_B -8.5237 1.9928 68 -4.28 <.0001 Tukey-Kramer 0.0033 0.05 -12.5003 -4.5470 -15.2682 -1.7792
donorgroup*region Ins. pos. T1D 2_B No diabetes 3_T -9.3541 2.1009 68 -4.45 <.0001 Tukey-Kramer 0.0018 0.05 -13.5464 -5.1618 -16.4643 -2.2438
donorgroup*region Ins. pos. T1D 3_T No diabetes 1_H -6.8806 2.0414 68 -3.37 0.0012 Tukey-Kramer 0.0519 0.05 -10.9542 -2.8071 -13.7895 0.02824
donorgroup*region Ins. pos. T1D 3_T No diabetes 2_B -7.1154 2.1599 68 -3.29 0.0016 Tukey-Kramer 0.0635 0.05 -11.4255 -2.8054 -14.4255 0.1946
donorgroup*region Ins. pos. T1D 3_T No diabetes 3_T -7.9458 2.2600 68 -3.52 0.0008 Tukey-Kramer 0.0348 0.05 -12.4557 -3.4360 -15.5946 -0.2971
donorgroup*region No diabetes 1_H No diabetes 2_B -0.2348 0.9619 68 -0.24 0.8079 Tukey-Kramer 1.0000 0.05 -2.1544 1.6847 -3.4904 3.0208
donorgroup*region No diabetes 1_H No diabetes 3_T -1.0652 1.0448 68 -1.02 0.3115 Tukey-Kramer 0.9967 0.05 -3.1500 1.0196 -4.6011 2.4707
donorgroup*region No diabetes 2_B No diabetes 3_T -0.8304 1.0982 68 -0.76 0.4522 Tukey-Kramer 0.9998 0.05 -3.0219 1.3611 -4.5473 2.8865
In [139]:
%explore(acinar_density);
Out[139]:
SAS Output

SAS Output

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable acinar_density
Covariance Structure Variance Components
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method Parameter
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 1
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 1767.15952354  
1 1 1767.15952354 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
region nPODCaseI(donorgrou) 1276781

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 1767.2
AIC (Smaller is Better) 1769.2
AICC (Smaller is Better) 1769.2
BIC (Smaller is Better) 1770.8

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
0 0.00 1.0000

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     8629.08 301.99 35 28.57 <.0001
region   PB 135.90 435.22 68 0.31 0.7558
region   PH 163.29 427.08 68 0.38 0.7034
region   PT 0 . . . .
donorgroup Autoab Pos   186.13 500.80 35 0.37 0.7124
donorgroup Ins. neg. T1D   80.2483 523.06 35 0.15 0.8789
donorgroup Ins. pos. T1D   1330.13 467.84 35 2.84 0.0074
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB -117.26 713.17 68 -0.16 0.8699
donorgroup*region Autoab Pos PH -47.9864 724.15 68 -0.07 0.9474
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB 353.83 744.45 68 0.48 0.6361
donorgroup*region Ins. neg. T1D PH -126.56 739.72 68 -0.17 0.8647
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 84.4322 666.91 68 0.13 0.8996
donorgroup*region Ins. pos. T1D PH -226.57 661.63 68 -0.34 0.7331
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 0.35 0.7064
donorgroup 3 35 8.57 0.0002
donorgroup*region 6 68 0.13 0.9926

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable acinar_density
Covariance Structure Compound Symmetry
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method Profile
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 2
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 1767.15952354  
1 2 1679.24092672 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
CS nPODCaseI(donorgrou) 1061325
Residual   214083

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 1679.2
AIC (Smaller is Better) 1683.2
AICC (Smaller is Better) 1683.4
BIC (Smaller is Better) 1686.6

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
1 87.92 <.0001

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     8629.08 301.83 35 28.59 <.0001
region   PB 65.2635 179.70 68 0.36 0.7176
region   PH 163.29 174.88 68 0.93 0.3538
region   PT 0 . . . .
donorgroup Autoab Pos   186.13 500.53 35 0.37 0.7122
donorgroup Ins. neg. T1D   80.2483 522.78 35 0.15 0.8789
donorgroup Ins. pos. T1D   1330.13 467.59 35 2.84 0.0074
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB -46.6212 292.94 68 -0.16 0.8740
donorgroup*region Autoab Pos PH 78.0628 299.44 68 0.26 0.7951
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB 424.47 305.71 68 1.39 0.1695
donorgroup*region Ins. neg. T1D PH -126.56 302.90 68 -0.42 0.6774
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 155.07 274.06 68 0.57 0.5734
donorgroup*region Ins. pos. T1D PH -226.57 270.92 68 -0.84 0.4059
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 1.66 0.1975
donorgroup 3 35 3.27 0.0325
donorgroup*region 6 68 1.04 0.4061

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable acinar_density
Covariance Structure Unstructured
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 6
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 1767.15952354  
1 2 1668.04903252 0.00000027
2 1 1668.04883272 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
UN(1,1) nPODCaseI(donorgrou) 1723653
UN(2,1) nPODCaseI(donorgrou) 1154122
UN(2,2) nPODCaseI(donorgrou) 1036753
UN(3,1) nPODCaseI(donorgrou) 1188865
UN(3,2) nPODCaseI(donorgrou) 855075
UN(3,3) nPODCaseI(donorgrou) 1079737

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 1668.0
AIC (Smaller is Better) 1680.0
AICC (Smaller is Better) 1680.9
BIC (Smaller is Better) 1690.0

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
5 99.11 <.0001

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     8629.08 277.71 35 31.07 <.0001
region   PB 40.5185 178.86 35 0.23 0.8221
region   PH 163.29 170.37 35 0.96 0.3444
region   PT 0 . . . .
donorgroup Autoab Pos   186.13 460.53 35 0.40 0.6886
donorgroup Ins. neg. T1D   80.2483 481.01 35 0.17 0.8685
donorgroup Ins. pos. T1D   1330.13 430.23 35 3.09 0.0039
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB -21.8762 291.89 35 -0.07 0.9407
donorgroup*region Autoab Pos PH 63.9433 290.33 35 0.22 0.8270
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB 449.21 304.63 35 1.47 0.1493
donorgroup*region Ins. neg. T1D PH -126.56 295.08 35 -0.43 0.6706
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 179.81 273.05 35 0.66 0.5145
donorgroup*region Ins. pos. T1D PH -226.57 263.93 35 -0.86 0.3965
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 35 1.57 0.2222
donorgroup 3 35 3.29 0.0318
donorgroup*region 6 35 1.02 0.4272

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable acinar_density
Covariance Structure Unstructured using Correlations
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 6
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 1767.15952354  
1 2 1668.05039374 0.00000210
2 1 1668.05023624 0.00000189
3 1 1668.05023622 0.00000189
4 0 1668.05023622 0.00000189
5 0 1668.05023622 0.00000189
6 0 1668.05023622 0.00000189
7 1 1668.05023622 0.00000189
8 1 1668.05023618 0.00000189
9 1 1668.05023575 0.00000189
10 1 1668.05023147 0.00000189
11 1 1668.05018970 0.00000183
12 1 1668.05016419 0.00000180
13 1 1668.05013917 0.00000176
14 1 1668.05011464 0.00000173
15 1 1668.05009060 0.00000170
16 1 1668.05006702 0.00000167
17 1 1668.05004391 0.00000163
18 1 1668.05002125 0.00000160
19 1 1668.04999903 0.00000157
20 1 1668.04997724 0.00000154
21 1 1668.04995589 0.00000152
22 1 1668.04993495 0.00000149
23 1 1668.04991442 0.00000146
24 1 1668.04989429 0.00000143
25 1 1668.04987456 0.00000141
26 1 1668.04985521 0.00000138
27 1 1668.04983624 0.00000135
28 1 1668.04981764 0.00000133
29 1 1668.04979941 0.00000130
30 1 1668.04978153 0.00000128
31 1 1668.04976400 0.00000126
32 1 1668.04974682 0.00000123
33 1 1668.04972997 0.00000121
34 1 1668.04971345 0.00000119
35 1 1668.04969725 0.00000117
36 1 1668.04968138 0.00000115
37 1 1668.04966581 0.00000112
38 1 1668.04965054 0.00000110
39 1 1668.04963558 0.00000108
40 1 1668.04962090 0.00000106
41 1 1668.04960652 0.00000104
42 1 1668.04959241 0.00000103
43 1 1668.04957858 0.00000101
44 1 1668.04956502 0.00000099
45 1 1668.04955173 0.00000097
46 1 1668.04953869 0.00000095
47 1 1668.04952591 0.00000094
48 1 1668.04951338 0.00000092
49 1 1668.04950110 0.00000090
50 1 1668.04948905 0.00000089

Convergence Status

WARNING: Did not converge.

Covariance Parameter Values At Last Iteration

Covariance Parameter Values At Last Iteration
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 1718332
Var(2) nPODCaseI(donorgrou) 1037903
Var(3) nPODCaseI(donorgrou) 1079203
Corr(2,1) nPODCaseI(donorgrou) 0.8632
Corr(3,1) nPODCaseI(donorgrou) 0.8713
Corr(3,2) nPODCaseI(donorgrou) 0.8081

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable acinar_density
Covariance Structure Banded
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 6
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 45 1767.15952354  
1 44 131508687.58583 0.49999931
2 44 131508687.58582 0.49999931

Convergence Status

WARNING: Stopped because of too many likelihood evaluations.

Covariance Parameter Values At Last Iteration

Covariance Parameter Values At Last Iteration
Cov Parm Subject Estimate
UN(1,1) nPODCaseI(donorgrou) 1.0000
UN(2,1) nPODCaseI(donorgrou) 0
UN(2,2) nPODCaseI(donorgrou) 1.0000
UN(3,1) nPODCaseI(donorgrou) 0
UN(3,2) nPODCaseI(donorgrou) 0
UN(3,3) nPODCaseI(donorgrou) 1.0000

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable acinar_density
Covariance Structure Heterogeneous Compound Symmetry
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 4
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 1767.15952354  
1 2 1670.54520044 0.00004958
2 1 1670.54363425 0.00004784
3 1 1670.54363384 0.00004785
4 0 1670.54363384 0.00004785
5 0 1670.54363384 0.00004785
6 1 1670.54363383 0.00004785
7 1 1670.54363378 0.00004785
8 1 1670.54363329 0.00004785
9 1 1670.54362839 0.00004784
10 1 1670.54357944 0.00004778
11 1 1670.54309545 0.00004711
12 1 1670.54192204 0.00004549
13 1 1670.54079039 0.00004393
14 1 1670.53969898 0.00004243
15 1 1670.53864636 0.00004098
16 1 1670.53763111 0.00003958
17 1 1670.53665190 0.00003824
18 1 1670.53570741 0.00003694
19 1 1670.53479640 0.00003568
20 1 1670.53391765 0.00003447
21 1 1670.53307000 0.00003331
22 1 1670.53225234 0.00003218
23 1 1670.53146359 0.00003110
24 1 1670.53070270 0.00003005
25 1 1670.52996868 0.00002904
26 1 1670.52926056 0.00002807
27 1 1670.52857741 0.00002713
28 1 1670.52791833 0.00002622
29 1 1670.52728248 0.00002535
30 1 1670.52666900 0.00002450
31 1 1670.52607711 0.00002369
32 1 1670.52550603 0.00002290
33 1 1670.52495501 0.00002215
34 1 1670.52442335 0.00002142
35 1 1670.52391035 0.00002071
36 1 1670.52341534 0.00002003
37 1 1670.52293768 0.00001937
38 1 1670.52247676 0.00001874
39 1 1670.52203198 0.00001813
40 1 1670.52160277 0.00001754
41 1 1670.52118856 0.00001697
42 1 1670.52078884 0.00001642
43 1 1670.52040307 0.00001589
44 1 1670.52003078 0.00001538
45 1 1670.51967147 0.00001489
46 1 1670.51932469 0.00001441
47 1 1670.51899000 0.00001395
48 1 1670.51866696 0.00001351
49 1 1670.51835516 0.00001308
50 1 1670.51805421 0.00001266

Convergence Status

WARNING: Did not converge.

Covariance Parameter Values At Last Iteration

Covariance Parameter Values At Last Iteration
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 1706156
Var(2) nPODCaseI(donorgrou) 1047901
Var(3) nPODCaseI(donorgrou) 1087821
CSH nPODCaseI(donorgrou) 0.8477

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable acinar_density
Covariance Structure Huynh-Feldt
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 4
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 1767.15952354  
1 2 1668.18071737 0.00000011
2 1 1668.18063799 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 1678560
Var(2) nPODCaseI(donorgrou) 1043695
Var(3) nPODCaseI(donorgrou) 1070563
HF nPODCaseI(donorgrou) 213775

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 1668.2
AIC (Smaller is Better) 1676.2
AICC (Smaller is Better) 1676.6
BIC (Smaller is Better) 1682.8

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
3 98.98 <.0001

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     8629.08 276.53 35 31.20 <.0001
region   PB 41.5159 179.06 68 0.23 0.8173
region   PH 163.29 174.75 68 0.93 0.3534
region   PT 0 . . . .
donorgroup Autoab Pos   186.13 458.57 35 0.41 0.6873
donorgroup Ins. neg. T1D   80.2483 478.96 35 0.17 0.8679
donorgroup Ins. pos. T1D   1330.13 428.40 35 3.10 0.0038
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB -22.8737 292.41 68 -0.08 0.9379
donorgroup*region Autoab Pos PH 66.7476 297.40 68 0.22 0.8231
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB 448.22 305.19 68 1.47 0.1465
donorgroup*region Ins. neg. T1D PH -126.56 302.68 68 -0.42 0.6772
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 178.82 273.52 68 0.65 0.5155
donorgroup*region Ins. pos. T1D PH -226.57 270.73 68 -0.84 0.4056
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 1.57 0.2160
donorgroup 3 35 3.33 0.0304
donorgroup*region 6 68 1.08 0.3831

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable acinar_density
Covariance Structure Heterogeneous Autoregressive
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 4
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 1767.15952354  
1 2 1683.52816823 0.00029579
2 1 1683.38392221 0.00012472
3 1 1683.38197222 0.00012307
4 1 1683.38197178 0.00012309
5 0 1683.38197178 0.00012309
6 1 1683.38197177 0.00012309
7 1 1683.38197167 0.00012309
8 1 1683.38197061 0.00012308
9 1 1683.38196006 0.00012307
10 1 1683.38185467 0.00012293
11 1 1683.38081254 0.00012156
12 1 1683.37828523 0.00011824
13 1 1683.37584601 0.00011503
14 1 1683.37349079 0.00011192
15 1 1683.37121573 0.00010892
16 1 1683.36901722 0.00010601
17 1 1683.36689187 0.00010320
18 1 1683.36483648 0.00010047
19 1 1683.36284803 0.00009783
20 1 1683.36092369 0.00009527
21 1 1683.35906079 0.00009279
22 1 1683.35725678 0.00009039
23 1 1683.35550929 0.00008806
24 1 1683.35381605 0.00008580
25 1 1683.35217492 0.00008360
26 1 1683.35058387 0.00008147
27 1 1683.34904099 0.00007941
28 1 1683.34754444 0.00007740
29 1 1683.34609250 0.00007545
30 1 1683.34468353 0.00007356
31 1 1683.34331595 0.00007172
32 1 1683.34198828 0.00006994
33 1 1683.34069910 0.00006820
34 1 1683.33944706 0.00006652
35 1 1683.33823086 0.00006488
36 1 1683.33704929 0.00006328
37 1 1683.33590116 0.00006173
38 1 1683.33478536 0.00006023
39 1 1683.33370080 0.00005876
40 1 1683.33264645 0.00005733
41 1 1683.33162134 0.00005595
42 1 1683.33062453 0.00005460
43 1 1683.32965509 0.00005328
44 1 1683.32871218 0.00005201
45 1 1683.32779494 0.00005076
46 1 1683.32690260 0.00004955
47 1 1683.32603436 0.00004837
48 1 1683.32518950 0.00004723
49 1 1683.32436731 0.00004611
50 1 1683.32356709 0.00004502

Convergence Status

WARNING: Did not converge.

Covariance Parameter Values At Last Iteration

Covariance Parameter Values At Last Iteration
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 1701635
Var(2) nPODCaseI(donorgrou) 1040326
Var(3) nPODCaseI(donorgrou) 1101037
ARH(1) nPODCaseI(donorgrou) 0.8363

The SAS System

The PRINT Procedure

Data Set WORK.ALL

Description arh1 cs csh hf un unr vc
-2 Res Log Likelihood 593.5 1679.2 587.9 1668.2 1668.0 587.9 1767.2
AIC (Smaller is Better) 601.5 1683.2 595.9 1676.2 1680.0 599.9 1769.2
AICC (Smaller is Better) 601.9 1683.4 596.3 1676.6 1680.9 600.8 1769.2
BIC (Smaller is Better) 608.2 1686.6 602.6 1682.8 1690.0 609.9 1770.8

The SAS System

The PRINT Procedure

Data Set WORK.STATUS

Obs Reason Status pdG pdH covar
1 WARNING: Did not converge. 1 1 1 arh(1)
2 Convergence criteria met. 0 1 1 cs
3 WARNING: Did not converge. 1 1 1 csh
4 Convergence criteria met. 0 1 1 hf
5 Convergence criteria met. 0 1 1 un
6 WARNING: Stopped because of too many likelihood evaluations. 1 1 1 un1
7 WARNING: Did not converge. 1 1 1 unr
8 Convergence criteria met. 0 1 1 vc
In [140]:
PROC mixed data=cell3 /*maxiter=1000 maxfunc=5000  can also use covtest*/;
     format region $regionformat.;
     class nPODCaseID donorgroup region;
     model  acinar_density =region|donorgroup/solution; /*can use  ddfm = kenwardroger after solution for unbalanced data to improve performance of t and f tests*/
     /*option e3 after solution helps to describe how type 3 tests were constructed*/
     repeated  region/ subject=nPODCaseID(donorgroup)  type=un; 
     lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;
run;
Out[140]:
SAS Output

SAS Output

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable acinar_density
Covariance Structure Unstructured
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 1_H 2_B 3_T

Dimensions

Dimensions
Covariance Parameters 6
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 1767.15952354  
1 2 1668.04903252 0.00000027
2 1 1668.04883272 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
UN(1,1) nPODCaseI(donorgrou) 1036753
UN(2,1) nPODCaseI(donorgrou) 1154122
UN(2,2) nPODCaseI(donorgrou) 1723653
UN(3,1) nPODCaseI(donorgrou) 855075
UN(3,2) nPODCaseI(donorgrou) 1188865
UN(3,3) nPODCaseI(donorgrou) 1079737

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 1668.0
AIC (Smaller is Better) 1680.0
AICC (Smaller is Better) 1680.9
BIC (Smaller is Better) 1690.0

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
5 99.11 <.0001

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     8629.08 277.71 35 31.07 <.0001
region   1_H 163.29 170.37 35 0.96 0.3444
region   2_B 40.5185 178.86 35 0.23 0.8221
region   3_T 0 . . . .
donorgroup Autoab Pos   186.13 460.53 35 0.40 0.6886
donorgroup Ins. neg. T1D   80.2483 481.01 35 0.17 0.8685
donorgroup Ins. pos. T1D   1330.13 430.23 35 3.09 0.0039
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos 1_H 63.9433 290.33 35 0.22 0.8270
donorgroup*region Autoab Pos 2_B -21.8762 291.89 35 -0.07 0.9407
donorgroup*region Autoab Pos 3_T 0 . . . .
donorgroup*region Ins. neg. T1D 1_H -126.56 295.08 35 -0.43 0.6706
donorgroup*region Ins. neg. T1D 2_B 449.21 304.63 35 1.47 0.1493
donorgroup*region Ins. neg. T1D 3_T 0 . . . .
donorgroup*region Ins. pos. T1D 1_H -226.57 263.93 35 -0.86 0.3965
donorgroup*region Ins. pos. T1D 2_B 179.81 273.05 35 0.66 0.5145
donorgroup*region Ins. pos. T1D 3_T 0 . . . .
donorgroup*region No diabetes 1_H 0 . . . .
donorgroup*region No diabetes 2_B 0 . . . .
donorgroup*region No diabetes 3_T 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 35 1.57 0.2222
donorgroup 3 35 3.29 0.0318
donorgroup*region 6 35 1.02 0.4272

Least Squares Means

Least Squares Means
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t| Alpha Lower Upper
region   1_H 9119.20 169.54 35 53.79 <.0001 0.05 8775.01 9463.38
region   2_B 9220.51 217.77 35 42.34 <.0001 0.05 8778.42 9662.60
region   3_T 9028.20 172.18 35 52.44 <.0001 0.05 8678.67 9377.74
donorgroup Autoab Pos   8897.16 377.71 35 23.56 <.0001 0.05 8130.36 9663.96
donorgroup Ins. neg. T1D   8884.81 403.09 35 22.04 <.0001 0.05 8066.50 9703.13
donorgroup Ins. pos. T1D   10012 337.25 35 29.69 <.0001 0.05 9326.91 10696
donorgroup No diabetes   8697.01 285.34 35 30.48 <.0001 0.05 8117.75 9276.28
donorgroup*region Autoab Pos 1_H 9042.44 366.15 35 24.70 <.0001 0.05 8299.10 9785.77
donorgroup*region Autoab Pos 2_B 8833.84 464.17 35 19.03 <.0001 0.05 7891.52 9776.17
donorgroup*region Autoab Pos 3_T 8815.20 367.38 35 23.99 <.0001 0.05 8069.38 9561.02
donorgroup*region Ins. neg. T1D 1_H 8746.05 384.85 35 22.73 <.0001 0.05 7964.77 9527.33
donorgroup*region Ins. neg. T1D 2_B 9199.06 496.22 35 18.54 <.0001 0.05 8191.67 10206
donorgroup*region Ins. neg. T1D 3_T 8709.32 392.74 35 22.18 <.0001 0.05 7912.01 9506.64
donorgroup*region Ins. pos. T1D 1_H 9895.93 321.99 35 30.73 <.0001 0.05 9242.27 10550
donorgroup*region Ins. pos. T1D 2_B 10180 415.17 35 24.52 <.0001 0.05 9336.70 11022
donorgroup*region Ins. pos. T1D 3_T 9959.21 328.59 35 30.31 <.0001 0.05 9292.13 10626
donorgroup*region No diabetes 1_H 8792.37 272.13 35 32.31 <.0001 0.05 8239.92 9344.82
donorgroup*region No diabetes 2_B 8669.59 353.14 35 24.55 <.0001 0.05 7952.69 9386.50
donorgroup*region No diabetes 3_T 8629.08 277.71 35 31.07 <.0001 0.05 8065.29 9192.86

Differences of Least Squares Means

Differences of Least Squares Means
Effect donorgroup region _donorgroup region Estimate Standard
Error
DF t Value Pr > |t| Adjustment Adj P Alpha Lower Upper Adj Lower Adj Upper
region   1_H   2_B -101.31 113.11 35 -0.90 0.3765 Tukey-Kramer 0.6466 0.05 -330.93 128.31 -378.12 175.49
region   1_H   3_T 90.9939 106.94 35 0.85 0.4006 Tukey-Kramer 0.6743 0.05 -126.10 308.09 -170.71 352.70
region   2_B   3_T 192.31 108.56 35 1.77 0.0852 Tukey-Kramer 0.1940 0.05 -28.0877 412.70 -73.3761 457.99
donorgroup Autoab Pos   Ins. neg. T1D   12.3488 552.40 35 0.02 0.9823 Tukey-Kramer 1.0000 0.05 -1109.09 1133.78 -1477.43 1502.12
donorgroup Autoab Pos   Ins. pos. T1D   -1114.40 506.36 35 -2.20 0.0344 Tukey-Kramer 0.1429 0.05 -2142.37 -86.4271 -2480.01 251.21
donorgroup Autoab Pos   No diabetes   200.15 473.38 35 0.42 0.6750 Tukey-Kramer 0.9742 0.05 -760.85 1161.15 -1076.50 1476.80
donorgroup Ins. neg. T1D   Ins. pos. T1D   -1126.75 525.56 35 -2.14 0.0391 Tukey-Kramer 0.1594 0.05 -2193.70 -59.7980 -2544.14 290.65
donorgroup Ins. neg. T1D   No diabetes   187.80 493.86 35 0.38 0.7060 Tukey-Kramer 0.9810 0.05 -814.79 1190.39 -1144.09 1519.69
donorgroup Ins. pos. T1D   No diabetes   1314.55 441.76 35 2.98 0.0053 Tukey-Kramer 0.0259 0.05 417.72 2211.37 123.16 2505.93
donorgroup*region Autoab Pos 1_H Autoab Pos 2_B 208.59 246.97 35 0.84 0.4041 Tukey-Kramer 0.9993 0.05 -292.79 709.97 -655.02 1072.21
donorgroup*region Autoab Pos 1_H Autoab Pos 3_T 227.23 235.09 35 0.97 0.3404 Tukey-Kramer 0.9975 0.05 -250.02 704.49 -594.83 1049.30
donorgroup*region Autoab Pos 1_H Ins. neg. T1D 1_H 296.38 531.20 35 0.56 0.5804 Tukey-Kramer 1.0000 0.05 -782.02 1374.78 -1561.14 2153.91
donorgroup*region Autoab Pos 1_H Ins. neg. T1D 2_B -156.62 616.69 35 -0.25 0.8010 Tukey-Kramer 1.0000 0.05 -1408.57 1095.32 -2313.08 1999.83
donorgroup*region Autoab Pos 1_H Ins. neg. T1D 3_T 333.11 536.95 35 0.62 0.5390 Tukey-Kramer 1.0000 0.05 -756.96 1423.18 -1544.52 2210.74
donorgroup*region Autoab Pos 1_H Ins. pos. T1D 1_H -853.50 487.59 35 -1.75 0.0888 Tukey-Kramer 0.8324 0.05 -1843.36 136.36 -2558.52 851.52
donorgroup*region Autoab Pos 1_H Ins. pos. T1D 2_B -1137.10 553.56 35 -2.05 0.0475 Tukey-Kramer 0.6558 0.05 -2260.90 -13.3082 -3072.83 798.62
donorgroup*region Autoab Pos 1_H Ins. pos. T1D 3_T -916.77 491.98 35 -1.86 0.0708 Tukey-Kramer 0.7725 0.05 -1915.54 81.9950 -2637.14 803.59
donorgroup*region Autoab Pos 1_H No diabetes 1_H 250.07 456.20 35 0.55 0.5871 Tukey-Kramer 1.0000 0.05 -676.07 1176.21 -1345.20 1845.34
donorgroup*region Autoab Pos 1_H No diabetes 2_B 372.84 508.70 35 0.73 0.4685 Tukey-Kramer 0.9998 0.05 -659.87 1405.55 -1405.99 2151.67
donorgroup*region Autoab Pos 1_H No diabetes 3_T 413.36 459.56 35 0.90 0.3745 Tukey-Kramer 0.9987 0.05 -519.59 1346.31 -1193.63 2020.35
donorgroup*region Autoab Pos 2_B Autoab Pos 3_T 18.6423 230.67 35 0.08 0.9360 Tukey-Kramer 1.0000 0.05 -449.64 486.92 -787.96 825.25
donorgroup*region Autoab Pos 2_B Ins. neg. T1D 1_H 87.7917 602.96 35 0.15 0.8851 Tukey-Kramer 1.0000 0.05 -1136.29 1311.87 -2020.67 2196.25
donorgroup*region Autoab Pos 2_B Ins. neg. T1D 2_B -365.21 679.48 35 -0.54 0.5943 Tukey-Kramer 1.0000 0.05 -1744.63 1014.20 -2741.24 2010.81
donorgroup*region Autoab Pos 2_B Ins. neg. T1D 3_T 124.52 608.03 35 0.20 0.8389 Tukey-Kramer 1.0000 0.05 -1109.85 1358.89 -2001.67 2250.71
donorgroup*region Autoab Pos 2_B Ins. pos. T1D 1_H -1062.09 564.92 35 -1.88 0.0684 Tukey-Kramer 0.7629 0.05 -2208.93 84.7558 -3037.51 913.33
donorgroup*region Autoab Pos 2_B Ins. pos. T1D 2_B -1345.69 622.75 35 -2.16 0.0376 Tukey-Kramer 0.5860 0.05 -2609.95 -81.4381 -3523.36 831.97
donorgroup*region Autoab Pos 2_B Ins. pos. T1D 3_T -1125.36 568.71 35 -1.98 0.0557 Tukey-Kramer 0.7036 0.05 -2279.91 29.1776 -3114.05 863.32
donorgroup*region Autoab Pos 2_B No diabetes 1_H 41.4779 538.06 35 0.08 0.9390 Tukey-Kramer 1.0000 0.05 -1050.85 1133.80 -1840.03 1922.99
donorgroup*region Autoab Pos 2_B No diabetes 2_B 164.25 583.23 35 0.28 0.7799 Tukey-Kramer 1.0000 0.05 -1019.78 1348.28 -1875.22 2203.72
donorgroup*region Autoab Pos 2_B No diabetes 3_T 204.77 540.91 35 0.38 0.7073 Tukey-Kramer 1.0000 0.05 -893.33 1302.87 -1686.69 2096.23
donorgroup*region Autoab Pos 3_T Ins. neg. T1D 1_H 69.1494 532.05 35 0.13 0.8973 Tukey-Kramer 1.0000 0.05 -1010.96 1149.26 -1791.33 1929.63
donorgroup*region Autoab Pos 3_T Ins. neg. T1D 2_B -383.86 617.42 35 -0.62 0.5382 Tukey-Kramer 1.0000 0.05 -1637.28 869.57 -2542.86 1775.15
donorgroup*region Autoab Pos 3_T Ins. neg. T1D 3_T 105.88 537.79 35 0.20 0.8451 Tukey-Kramer 1.0000 0.05 -985.89 1197.64 -1774.68 1986.43
donorgroup*region Autoab Pos 3_T Ins. pos. T1D 1_H -1080.73 488.51 35 -2.21 0.0336 Tukey-Kramer 0.5522 0.05 -2072.46 -89.0014 -2788.97 627.51
donorgroup*region Autoab Pos 3_T Ins. pos. T1D 2_B -1364.34 554.38 35 -2.46 0.0189 Tukey-Kramer 0.3952 0.05 -2489.78 -238.89 -3302.90 574.22
donorgroup*region Autoab Pos 3_T Ins. pos. T1D 3_T -1144.01 492.89 35 -2.32 0.0262 Tukey-Kramer 0.4816 0.05 -2144.63 -143.39 -2867.56 579.55
donorgroup*region Autoab Pos 3_T No diabetes 1_H 22.8357 457.19 35 0.05 0.9604 Tukey-Kramer 1.0000 0.05 -905.31 950.98 -1575.87 1621.55
donorgroup*region Autoab Pos 3_T No diabetes 2_B 145.61 509.58 35 0.29 0.7768 Tukey-Kramer 1.0000 0.05 -888.90 1180.11 -1636.31 1927.53
donorgroup*region Autoab Pos 3_T No diabetes 3_T 186.13 460.53 35 0.40 0.6886 Tukey-Kramer 1.0000 0.05 -748.81 1121.06 -1424.28 1796.54
donorgroup*region Ins. neg. T1D 1_H Ins. neg. T1D 2_B -453.01 254.15 35 -1.78 0.0834 Tukey-Kramer 0.8164 0.05 -968.97 62.9559 -1341.74 435.73
donorgroup*region Ins. neg. T1D 1_H Ins. neg. T1D 3_T 36.7279 240.93 35 0.15 0.8797 Tukey-Kramer 1.0000 0.05 -452.39 525.85 -805.77 879.23
donorgroup*region Ins. neg. T1D 1_H Ins. pos. T1D 1_H -1149.88 501.78 35 -2.29 0.0281 Tukey-Kramer 0.5005 0.05 -2168.55 -131.21 -2904.52 604.76
donorgroup*region Ins. neg. T1D 1_H Ins. pos. T1D 2_B -1433.49 566.10 35 -2.53 0.0160 Tukey-Kramer 0.3543 0.05 -2582.74 -284.24 -3413.06 546.08
donorgroup*region Ins. neg. T1D 1_H Ins. pos. T1D 3_T -1213.16 506.04 35 -2.40 0.0220 Tukey-Kramer 0.4337 0.05 -2240.48 -185.83 -2982.71 556.40
donorgroup*region Ins. neg. T1D 1_H No diabetes 1_H -46.3137 471.34 35 -0.10 0.9223 Tukey-Kramer 1.0000 0.05 -1003.18 910.56 -1694.51 1601.88
donorgroup*region Ins. neg. T1D 1_H No diabetes 2_B 76.4578 522.32 35 0.15 0.8845 Tukey-Kramer 1.0000 0.05 -983.90 1136.81 -1749.99 1902.91
donorgroup*region Ins. neg. T1D 1_H No diabetes 3_T 116.98 474.59 35 0.25 0.8067 Tukey-Kramer 1.0000 0.05 -846.48 1080.44 -1542.57 1776.52
donorgroup*region Ins. neg. T1D 2_B Ins. neg. T1D 3_T 489.73 246.59 35 1.99 0.0549 Tukey-Kramer 0.6991 0.05 -10.8790 990.35 -372.56 1352.03
donorgroup*region Ins. neg. T1D 2_B Ins. pos. T1D 1_H -696.87 591.53 35 -1.18 0.2467 Tukey-Kramer 0.9874 0.05 -1897.75 504.00 -2765.37 1371.62
donorgroup*region Ins. neg. T1D 2_B Ins. pos. T1D 2_B -980.48 646.99 35 -1.52 0.1386 Tukey-Kramer 0.9262 0.05 -2293.95 332.99 -3242.91 1281.95
donorgroup*region Ins. neg. T1D 2_B Ins. pos. T1D 3_T -760.15 595.16 35 -1.28 0.2099 Tukey-Kramer 0.9768 0.05 -1968.38 448.08 -2841.31 1321.01
donorgroup*region Ins. neg. T1D 2_B No diabetes 1_H 406.69 565.94 35 0.72 0.4772 Tukey-Kramer 0.9998 0.05 -742.23 1555.61 -1572.31 2385.70
donorgroup*region Ins. neg. T1D 2_B No diabetes 2_B 529.46 609.05 35 0.87 0.3906 Tukey-Kramer 0.9990 0.05 -706.97 1765.90 -1600.28 2659.21
donorgroup*region Ins. neg. T1D 2_B No diabetes 3_T 569.98 568.65 35 1.00 0.3231 Tukey-Kramer 0.9966 0.05 -584.43 1724.40 -1418.48 2558.45
donorgroup*region Ins. neg. T1D 3_T Ins. pos. T1D 1_H -1186.61 507.86 35 -2.34 0.0253 Tukey-Kramer 0.4717 0.05 -2217.62 -155.59 -2962.52 589.30
donorgroup*region Ins. neg. T1D 3_T Ins. pos. T1D 2_B -1470.21 571.50 35 -2.57 0.0145 Tukey-Kramer 0.3322 0.05 -2630.42 -310.01 -3468.66 528.23
donorgroup*region Ins. neg. T1D 3_T Ins. pos. T1D 3_T -1249.88 512.08 35 -2.44 0.0199 Tukey-Kramer 0.4072 0.05 -2289.45 -210.31 -3040.53 540.76
donorgroup*region Ins. neg. T1D 3_T No diabetes 1_H -83.0417 477.81 35 -0.17 0.8630 Tukey-Kramer 1.0000 0.05 -1053.05 886.96 -1753.86 1587.78
donorgroup*region Ins. neg. T1D 3_T No diabetes 2_B 39.7299 528.16 35 0.08 0.9405 Tukey-Kramer 1.0000 0.05 -1032.49 1111.95 -1807.16 1886.62
donorgroup*region Ins. neg. T1D 3_T No diabetes 3_T 80.2483 481.01 35 0.17 0.8685 Tukey-Kramer 1.0000 0.05 -896.26 1056.75 -1601.77 1762.27
donorgroup*region Ins. pos. T1D 1_H Ins. pos. T1D 2_B -283.61 212.64 35 -1.33 0.1909 Tukey-Kramer 0.9684 0.05 -715.29 148.08 -1027.18 459.96
donorgroup*region Ins. pos. T1D 1_H Ins. pos. T1D 3_T -63.2759 201.58 35 -0.31 0.7555 Tukey-Kramer 1.0000 0.05 -472.50 345.95 -768.16 641.61
donorgroup*region Ins. pos. T1D 1_H No diabetes 1_H 1103.57 421.58 35 2.62 0.0130 Tukey-Kramer 0.3084 0.05 247.71 1959.42 -370.63 2577.76
donorgroup*region Ins. pos. T1D 1_H No diabetes 2_B 1226.34 477.89 35 2.57 0.0147 Tukey-Kramer 0.3356 0.05 256.17 2196.51 -444.77 2897.45
donorgroup*region Ins. pos. T1D 1_H No diabetes 3_T 1266.86 425.21 35 2.98 0.0052 Tukey-Kramer 0.1578 0.05 403.64 2130.07 -220.02 2753.73
donorgroup*region Ins. pos. T1D 2_B Ins. pos. T1D 3_T 220.33 206.32 35 1.07 0.2929 Tukey-Kramer 0.9943 0.05 -198.51 639.17 -501.12 941.78
donorgroup*region Ins. pos. T1D 2_B No diabetes 1_H 1387.17 496.41 35 2.79 0.0084 Tukey-Kramer 0.2258 0.05 379.41 2394.93 -348.68 3123.02
donorgroup*region Ins. pos. T1D 2_B No diabetes 2_B 1509.94 545.04 35 2.77 0.0089 Tukey-Kramer 0.2361 0.05 403.45 2616.44 -395.98 3415.87
donorgroup*region Ins. pos. T1D 2_B No diabetes 3_T 1550.46 499.49 35 3.10 0.0038 Tukey-Kramer 0.1218 0.05 536.45 2564.48 -196.17 3297.09
donorgroup*region Ins. pos. T1D 3_T No diabetes 1_H 1166.84 426.65 35 2.73 0.0097 Tukey-Kramer 0.2517 0.05 300.70 2032.98 -325.07 2658.75
donorgroup*region Ins. pos. T1D 3_T No diabetes 2_B 1289.61 482.37 35 2.67 0.0113 Tukey-Kramer 0.2805 0.05 310.35 2268.87 -397.15 2976.38
donorgroup*region Ins. pos. T1D 3_T No diabetes 3_T 1330.13 430.23 35 3.09 0.0039 Tukey-Kramer 0.1251 0.05 456.72 2203.55 -174.31 2834.57
donorgroup*region No diabetes 1_H No diabetes 2_B 122.77 184.08 35 0.67 0.5092 Tukey-Kramer 0.9999 0.05 -250.93 496.47 -520.92 766.46
donorgroup*region No diabetes 1_H No diabetes 3_T 163.29 170.37 35 0.96 0.3444 Tukey-Kramer 0.9977 0.05 -182.57 509.15 -432.45 759.03
donorgroup*region No diabetes 2_B No diabetes 3_T 40.5185 178.86 35 0.23 0.8221 Tukey-Kramer 1.0000 0.05 -322.59 403.63 -584.93 665.97
In [141]:
%explore('acinar: Avg Cell Area (cell size'n);
Out[141]:
SAS Output

SAS Output

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable acinar: Avg Cell Area (cell size
Covariance Structure Variance Components
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method Parameter
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 1
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 657.58011302  
1 1 657.58011302 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
region nPODCaseI(donorgrou) 26.7688

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 657.6
AIC (Smaller is Better) 659.6
AICC (Smaller is Better) 659.6
BIC (Smaller is Better) 661.2

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
0 0.00 1.0000

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     75.3641 1.3828 35 54.50 <.0001
region   PB 0.1909 1.9928 68 0.10 0.9240
region   PH 0.3538 1.9555 68 0.18 0.8570
region   PT 0 . . . .
donorgroup Autoab Pos   -1.5028 2.2931 35 -0.66 0.5165
donorgroup Ins. neg. T1D   -0.5578 2.3950 35 -0.23 0.8172
donorgroup Ins. pos. T1D   -5.0828 2.1422 35 -2.37 0.0233
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB 1.1852 3.2655 68 0.36 0.7178
donorgroup*region Autoab Pos PH 0.8135 3.3158 68 0.25 0.8069
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB -4.0782 3.4087 68 -1.20 0.2357
donorgroup*region Ins. neg. T1D PH -1.8642 3.3871 68 -0.55 0.5839
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB -2.5722 3.0537 68 -0.84 0.4025
donorgroup*region Ins. pos. T1D PH -2.2982 3.0295 68 -0.76 0.4507
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 0.47 0.6261
donorgroup 3 35 10.57 <.0001
donorgroup*region 6 68 0.48 0.8205

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable acinar: Avg Cell Area (cell size
Covariance Structure Compound Symmetry
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method Profile
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 2
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 657.58011302  
1 2 598.42074993 0.00000291
2 1 598.42015030 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
CS nPODCaseI(donorgrou) 19.9459
Residual   7.0719

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 598.4
AIC (Smaller is Better) 602.4
AICC (Smaller is Better) 602.5
BIC (Smaller is Better) 605.7

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
1 59.16 <.0001

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     75.3641 1.3892 35 54.25 <.0001
region   PB 0.4764 1.0323 68 0.46 0.6459
region   PH 0.3538 1.0051 68 0.35 0.7259
region   PT 0 . . . .
donorgroup Autoab Pos   -1.5028 2.3037 35 -0.65 0.5184
donorgroup Ins. neg. T1D   -0.5578 2.4061 35 -0.23 0.8180
donorgroup Ins. pos. T1D   -5.0828 2.1521 35 -2.36 0.0239
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB 0.8996 1.6833 68 0.53 0.5948
donorgroup*region Autoab Pos PH -0.08098 1.7199 68 -0.05 0.9626
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB -4.3637 1.7567 68 -2.48 0.0155
donorgroup*region Ins. neg. T1D PH -1.8642 1.7409 68 -1.07 0.2880
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB -2.8578 1.5748 68 -1.81 0.0740
donorgroup*region Ins. pos. T1D PH -2.2982 1.5571 68 -1.48 0.1446
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 1.60 0.2099
donorgroup 3 35 4.26 0.0115
donorgroup*region 6 68 1.90 0.0932

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable acinar: Avg Cell Area (cell size
Covariance Structure Unstructured
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 6
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 657.58011302  
1 2 594.13372094 0.00000800
2 1 594.13208505 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
UN(1,1) nPODCaseI(donorgrou) 27.8944
UN(2,1) nPODCaseI(donorgrou) 20.3205
UN(2,2) nPODCaseI(donorgrou) 22.9514
UN(3,1) nPODCaseI(donorgrou) 21.3315
UN(3,2) nPODCaseI(donorgrou) 17.8547
UN(3,3) nPODCaseI(donorgrou) 29.8099

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 594.1
AIC (Smaller is Better) 606.1
AICC (Smaller is Better) 607.0
BIC (Smaller is Better) 616.1

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
5 63.45 <.0001

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     75.3641 1.4592 35 51.65 <.0001
region   PB 0.4528 1.0575 35 0.43 0.6711
region   PH 0.3538 1.1036 35 0.32 0.7504
region   PT 0 . . . .
donorgroup Autoab Pos   -1.5028 2.4198 35 -0.62 0.5386
donorgroup Ins. neg. T1D   -0.5578 2.5274 35 -0.22 0.8266
donorgroup Ins. pos. T1D   -5.0828 2.2606 35 -2.25 0.0309
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB 0.9233 1.7316 35 0.53 0.5973
donorgroup*region Autoab Pos PH -0.00648 1.8676 35 -0.00 0.9973
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB -4.3401 1.8075 35 -2.40 0.0218
donorgroup*region Ins. neg. T1D PH -1.8642 1.9115 35 -0.98 0.3361
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB -2.8341 1.6194 35 -1.75 0.0889
donorgroup*region Ins. pos. T1D PH -2.2982 1.7097 35 -1.34 0.1875
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 35 1.51 0.2357
donorgroup 3 35 4.28 0.0112
donorgroup*region 6 35 1.95 0.0999

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable acinar: Avg Cell Area (cell size
Covariance Structure Unstructured using Correlations
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 6
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 657.58011302  
1 2 594.13376969 0.00000822
2 1 594.13208522 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 27.8966
Var(2) nPODCaseI(donorgrou) 22.9530
Var(3) nPODCaseI(donorgrou) 29.8128
Corr(2,1) nPODCaseI(donorgrou) 0.8031
Corr(3,1) nPODCaseI(donorgrou) 0.7398
Corr(3,2) nPODCaseI(donorgrou) 0.6826

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 594.1
AIC (Smaller is Better) 606.1
AICC (Smaller is Better) 607.0
BIC (Smaller is Better) 616.1

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
5 63.45 <.0001

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     75.3641 1.4593 35 51.64 <.0001
region   PB 0.4528 1.0575 35 0.43 0.6711
region   PH 0.3538 1.1036 35 0.32 0.7504
region   PT 0 . . . .
donorgroup Autoab Pos   -1.5028 2.4199 35 -0.62 0.5386
donorgroup Ins. neg. T1D   -0.5578 2.5275 35 -0.22 0.8266
donorgroup Ins. pos. T1D   -5.0828 2.2607 35 -2.25 0.0310
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB 0.9233 1.7316 35 0.53 0.5973
donorgroup*region Autoab Pos PH -0.00649 1.8676 35 -0.00 0.9972
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB -4.3401 1.8075 35 -2.40 0.0218
donorgroup*region Ins. neg. T1D PH -1.8642 1.9115 35 -0.98 0.3361
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB -2.8341 1.6194 35 -1.75 0.0889
donorgroup*region Ins. pos. T1D PH -2.2982 1.7097 35 -1.34 0.1875
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 35 1.51 0.2357
donorgroup 3 35 4.28 0.0112
donorgroup*region 6 35 1.95 0.0999

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable acinar: Avg Cell Area (cell size
Covariance Structure Banded
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 6
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 44 657.58011302  
1 44 2973.18156505 0.46763565
2 44 2973.18156505 0.46763565

Convergence Status

WARNING: Stopped because of too many likelihood evaluations.

Covariance Parameter Values At Last Iteration

Covariance Parameter Values At Last Iteration
Cov Parm Subject Estimate
UN(1,1) nPODCaseI(donorgrou) 1.0000
UN(2,1) nPODCaseI(donorgrou) 0
UN(2,2) nPODCaseI(donorgrou) 1.0000
UN(3,1) nPODCaseI(donorgrou) 0
UN(3,2) nPODCaseI(donorgrou) 0
UN(3,3) nPODCaseI(donorgrou) 1.0000

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable acinar: Avg Cell Area (cell size
Covariance Structure Heterogeneous Compound Symmetry
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 4
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 657.58011302  
1 2 596.80748140 0.00001014
2 1 596.80539655 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 27.1807
Var(2) nPODCaseI(donorgrou) 22.8950
Var(3) nPODCaseI(donorgrou) 30.7536
CSH nPODCaseI(donorgrou) 0.7414

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 596.8
AIC (Smaller is Better) 604.8
AICC (Smaller is Better) 605.2
BIC (Smaller is Better) 611.5

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
3 60.77 <.0001

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     75.3641 1.4821 35 50.85 <.0001
region   PB 0.4668 1.0636 68 0.44 0.6621
region   PH 0.3538 1.0108 68 0.35 0.7274
region   PT 0 . . . .
donorgroup Autoab Pos   -1.5028 2.4578 35 -0.61 0.5449
donorgroup Ins. neg. T1D   -0.5578 2.5671 35 -0.22 0.8292
donorgroup Ins. pos. T1D   -5.0828 2.2961 35 -2.21 0.0335
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB 0.9093 1.7362 68 0.52 0.6022
donorgroup*region Autoab Pos PH 0.01464 1.7206 68 0.01 0.9932
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB -4.3541 1.8120 68 -2.40 0.0190
donorgroup*region Ins. neg. T1D PH -1.8642 1.7508 68 -1.06 0.2907
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB -2.8481 1.6241 68 -1.75 0.0840
donorgroup*region Ins. pos. T1D PH -2.2982 1.5659 68 -1.47 0.1468
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 1.48 0.2344
donorgroup 3 35 4.28 0.0112
donorgroup*region 6 68 1.80 0.1126

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable acinar: Avg Cell Area (cell size
Covariance Structure Huynh-Feldt
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 4
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 657.58011302  
1 2 597.04768754 0.00001529
2 1 597.04453428 0.00000001

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 30.6753
Var(2) nPODCaseI(donorgrou) 22.7140
Var(3) nPODCaseI(donorgrou) 28.1490
HF nPODCaseI(donorgrou) 7.0878

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 597.0
AIC (Smaller is Better) 605.0
AICC (Smaller is Better) 605.5
BIC (Smaller is Better) 611.7

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
3 60.54 <.0001

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     75.3641 1.4180 35 53.15 <.0001
region   PB 0.5163 1.0348 68 0.50 0.6194
region   PH 0.3538 1.0063 68 0.35 0.7262
region   PT 0 . . . .
donorgroup Autoab Pos   -1.5028 2.3514 35 -0.64 0.5269
donorgroup Ins. neg. T1D   -0.5578 2.4560 35 -0.23 0.8216
donorgroup Ins. pos. T1D   -5.0828 2.1967 35 -2.31 0.0267
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB 0.8597 1.6860 68 0.51 0.6118
donorgroup*region Autoab Pos PH 0.04112 1.7151 68 0.02 0.9809
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB -4.4036 1.7595 68 -2.50 0.0147
donorgroup*region Ins. neg. T1D PH -1.8642 1.7429 68 -1.07 0.2886
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB -2.8977 1.5774 68 -1.84 0.0706
donorgroup*region Ins. pos. T1D PH -2.2982 1.5589 68 -1.47 0.1450
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 1.55 0.2189
donorgroup 3 35 4.26 0.0115
donorgroup*region 6 68 1.91 0.0925

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable acinar: Avg Cell Area (cell size
Covariance Structure Heterogeneous Autoregressive
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 4
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 657.58011302  
1 2 603.31561066 0.00200427
2 1 602.85312789 0.00009076
3 1 602.83370818 0.00000028
4 1 602.83365066 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 26.0652
Var(2) nPODCaseI(donorgrou) 23.1615
Var(3) nPODCaseI(donorgrou) 31.7772
ARH(1) nPODCaseI(donorgrou) 0.7463

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 602.8
AIC (Smaller is Better) 610.8
AICC (Smaller is Better) 611.2
BIC (Smaller is Better) 617.5

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
3 54.75 <.0001

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     75.3641 1.5066 35 50.02 <.0001
region   PB 0.2754 1.3802 68 0.20 0.8425
region   PH 0.3538 1.0157 68 0.35 0.7287
region   PT 0 . . . .
donorgroup Autoab Pos   -1.5028 2.4984 35 -0.60 0.5514
donorgroup Ins. neg. T1D   -0.5578 2.6095 35 -0.21 0.8320
donorgroup Ins. pos. T1D   -5.0828 2.3340 35 -2.18 0.0363
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos PB 1.1007 2.2644 68 0.49 0.6285
donorgroup*region Autoab Pos PH -0.09429 1.7190 68 -0.05 0.9564
donorgroup*region Autoab Pos PT 0 . . . .
donorgroup*region Ins. neg. T1D PB -4.1626 2.3639 68 -1.76 0.0827
donorgroup*region Ins. neg. T1D PH -1.8642 1.7593 68 -1.06 0.2931
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB -2.6567 2.1173 68 -1.25 0.2139
donorgroup*region Ins. pos. T1D PH -2.2982 1.5736 68 -1.46 0.1488
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 68 0.96 0.3888
donorgroup 3 35 4.42 0.0097
donorgroup*region 6 68 1.14 0.3466

The SAS System

The PRINT Procedure

Data Set WORK.ALL

Description arh1 cs csh hf un unr vc
-2 Res Log Likelihood 602.8 598.4 596.8 597.0 594.1 594.1 657.6
AIC (Smaller is Better) 610.8 602.4 604.8 605.0 606.1 606.1 659.6
AICC (Smaller is Better) 611.2 602.5 605.2 605.5 607.0 607.0 659.6
BIC (Smaller is Better) 617.5 605.7 611.5 611.7 616.1 616.1 661.2

The SAS System

The PRINT Procedure

Data Set WORK.STATUS

Obs Reason Status pdG pdH covar
1 Convergence criteria met. 0 1 1 arh(1)
2 Convergence criteria met. 0 1 1 cs
3 Convergence criteria met. 0 1 1 csh
4 Convergence criteria met. 0 1 1 hf
5 Convergence criteria met. 0 1 1 un
6 WARNING: Stopped because of too many likelihood evaluations. 1 1 1 un1
7 Convergence criteria met. 0 1 1 unr
8 Convergence criteria met. 0 1 1 vc
In [142]:
PROC mixed data=cell3 /*maxiter=1000 maxfunc=5000  can also use covtest*/;
     format region $regionformat.;
     class nPODCaseID donorgroup region;
     model  'acinar: Avg Cell Area (cell size'n =region|donorgroup/solution; /*can use  ddfm = kenwardroger after solution for unbalanced data to improve performance of t and f tests*/
     /*option e3 after solution helps to describe how type 3 tests were constructed*/
     repeated  region/ subject=nPODCaseID(donorgroup)  type=un; 
     lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;
run;
Out[142]:
SAS Output

SAS Output

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.CELL3
Dependent Variable acinar: Avg Cell Area (cell size
Covariance Structure Unstructured
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 39 6062 6064 6079 6087 6089 6171 6195 6197 6228 6233 6237 6238 6243 6247 6265 6267 6278 6293 6318 6334 6339 6347 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6421 6424 6429 6445 6450 6472
donorgroup 4 Autoab Pos Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 1_H 2_B 3_T

Dimensions

Dimensions
Covariance Parameters 6
Columns in X 20
Columns in Z 0
Subjects 39
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 115
Number of Observations Used 115
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 657.58011302  
1 2 594.13372094 0.00000800
2 1 594.13208505 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
UN(1,1) nPODCaseI(donorgrou) 22.9514
UN(2,1) nPODCaseI(donorgrou) 20.3205
UN(2,2) nPODCaseI(donorgrou) 27.8944
UN(3,1) nPODCaseI(donorgrou) 17.8547
UN(3,2) nPODCaseI(donorgrou) 21.3315
UN(3,3) nPODCaseI(donorgrou) 29.8099

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 594.1
AIC (Smaller is Better) 606.1
AICC (Smaller is Better) 607.0
BIC (Smaller is Better) 616.1

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
5 63.45 <.0001

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     75.3641 1.4592 35 51.65 <.0001
region   1_H 0.3538 1.1036 35 0.32 0.7504
region   2_B 0.4528 1.0575 35 0.43 0.6711
region   3_T 0 . . . .
donorgroup Autoab Pos   -1.5028 2.4198 35 -0.62 0.5386
donorgroup Ins. neg. T1D   -0.5578 2.5274 35 -0.22 0.8266
donorgroup Ins. pos. T1D   -5.0828 2.2606 35 -2.25 0.0309
donorgroup No diabetes   0 . . . .
donorgroup*region Autoab Pos 1_H -0.00648 1.8676 35 -0.00 0.9973
donorgroup*region Autoab Pos 2_B 0.9233 1.7316 35 0.53 0.5973
donorgroup*region Autoab Pos 3_T 0 . . . .
donorgroup*region Ins. neg. T1D 1_H -1.8642 1.9115 35 -0.98 0.3361
donorgroup*region Ins. neg. T1D 2_B -4.3401 1.8075 35 -2.40 0.0218
donorgroup*region Ins. neg. T1D 3_T 0 . . . .
donorgroup*region Ins. pos. T1D 1_H -2.2982 1.7097 35 -1.34 0.1875
donorgroup*region Ins. pos. T1D 2_B -2.8341 1.6194 35 -1.75 0.0889
donorgroup*region Ins. pos. T1D 3_T 0 . . . .
donorgroup*region No diabetes 1_H 0 . . . .
donorgroup*region No diabetes 2_B 0 . . . .
donorgroup*region No diabetes 3_T 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 35 1.51 0.2357
donorgroup 3 35 4.28 0.0112
donorgroup*region 6 35 1.95 0.0999

Least Squares Means

Least Squares Means
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t| Alpha Lower Upper
region   1_H 72.8898 0.7992 35 91.20 <.0001 0.05 71.2672 74.5123
region   2_B 72.4683 0.8767 35 82.66 <.0001 0.05 70.6885 74.2481
region   3_T 73.5782 0.9047 35 81.33 <.0001 0.05 71.7416 75.4148
donorgroup Autoab Pos   74.4357 1.6699 35 44.57 <.0001 0.05 71.0456 77.8258
donorgroup Ins. neg. T1D   73.0070 1.7803 35 41.01 <.0001 0.05 69.3929 76.6211
donorgroup Ins. pos. T1D   68.8394 1.4895 35 46.22 <.0001 0.05 65.8156 71.8632
donorgroup No diabetes   75.6329 1.2608 35 59.99 <.0001 0.05 73.0734 78.1924
donorgroup*region Autoab Pos 1_H 74.2086 1.7342 35 42.79 <.0001 0.05 70.6880 77.7291
donorgroup*region Autoab Pos 2_B 75.2373 1.8673 35 40.29 <.0001 0.05 71.4465 79.0281
donorgroup*region Autoab Pos 3_T 73.8612 1.9303 35 38.26 <.0001 0.05 69.9424 77.7801
donorgroup*region Ins. neg. T1D 1_H 73.2958 1.8107 35 40.48 <.0001 0.05 69.6198 76.9718
donorgroup*region Ins. neg. T1D 2_B 70.9189 1.9962 35 35.53 <.0001 0.05 66.8664 74.9715
donorgroup*region Ins. neg. T1D 3_T 74.8062 2.0636 35 36.25 <.0001 0.05 70.6168 78.9956
donorgroup*region Ins. pos. T1D 1_H 68.3369 1.5150 35 45.11 <.0001 0.05 65.2613 71.4125
donorgroup*region Ins. pos. T1D 2_B 67.9000 1.6702 35 40.65 <.0001 0.05 64.5094 71.2906
donorgroup*region Ins. pos. T1D 3_T 70.2813 1.7266 35 40.71 <.0001 0.05 66.7762 73.7864
donorgroup*region No diabetes 1_H 75.7179 1.2804 35 59.14 <.0001 0.05 73.1186 78.3172
donorgroup*region No diabetes 2_B 75.8169 1.4270 35 53.13 <.0001 0.05 72.9199 78.7138
donorgroup*region No diabetes 3_T 75.3641 1.4592 35 51.65 <.0001 0.05 72.4017 78.3264

Differences of Least Squares Means

Differences of Least Squares Means
Effect donorgroup region _donorgroup region Estimate Standard
Error
DF t Value Pr > |t| Adjustment Adj P Alpha Lower Upper Adj Lower Adj Upper
region   1_H   2_B 0.4215 0.5400 35 0.78 0.4403 Tukey-Kramer 0.7172 0.05 -0.6747 1.5177 -0.8999 1.7430
region   1_H   3_T -0.6884 0.6905 35 -1.00 0.3256 Tukey-Kramer 0.5837 0.05 -2.0902 0.7134 -2.3783 1.0015
region   2_B   3_T -1.1099 0.6448 35 -1.72 0.0940 Tukey-Kramer 0.2115 0.05 -2.4189 0.1990 -2.6878 0.4679
donorgroup Autoab Pos   Ins. neg. T1D   1.4287 2.4409 35 0.59 0.5621 Tukey-Kramer 0.9358 0.05 -3.5266 6.3840 -5.1541 8.0115
donorgroup Autoab Pos   Ins. pos. T1D   5.5963 2.2377 35 2.50 0.0172 Tukey-Kramer 0.0773 0.05 1.0536 10.1390 -0.4384 11.6311
donorgroup Autoab Pos   No diabetes   -1.1972 2.0924 35 -0.57 0.5709 Tukey-Kramer 0.9397 0.05 -5.4450 3.0506 -6.8402 4.4458
donorgroup Ins. neg. T1D   Ins. pos. T1D   4.1676 2.3212 35 1.80 0.0812 Tukey-Kramer 0.2925 0.05 -0.5446 8.8799 -2.0924 10.4276
donorgroup Ins. neg. T1D   No diabetes   -2.6259 2.1815 35 -1.20 0.2368 Tukey-Kramer 0.6286 0.05 -7.0546 1.8027 -8.5092 3.2573
donorgroup Ins. pos. T1D   No diabetes   -6.7935 1.9514 35 -3.48 0.0014 Tukey-Kramer 0.0071 0.05 -10.7552 -2.8319 -12.0564 -1.5307
donorgroup*region Autoab Pos 1_H Autoab Pos 2_B -1.0287 1.1891 35 -0.87 0.3929 Tukey-Kramer 0.9991 0.05 -3.4428 1.3853 -5.1869 3.1294
donorgroup*region Autoab Pos 1_H Autoab Pos 3_T 0.3473 1.5066 35 0.23 0.8190 Tukey-Kramer 1.0000 0.05 -2.7113 3.4059 -4.9211 5.6157
donorgroup*region Autoab Pos 1_H Ins. neg. T1D 1_H 0.9127 2.5072 35 0.36 0.7180 Tukey-Kramer 1.0000 0.05 -4.1772 6.0027 -7.8546 9.6801
donorgroup*region Autoab Pos 1_H Ins. neg. T1D 2_B 3.2896 2.6443 35 1.24 0.2217 Tukey-Kramer 0.9809 0.05 -2.0786 8.6578 -5.9570 12.5363
donorgroup*region Autoab Pos 1_H Ins. neg. T1D 3_T -0.5977 2.6955 35 -0.22 0.8258 Tukey-Kramer 1.0000 0.05 -6.0699 4.8746 -10.0235 8.8282
donorgroup*region Autoab Pos 1_H Ins. pos. T1D 1_H 5.8717 2.3027 35 2.55 0.0153 Tukey-Kramer 0.3445 0.05 1.1969 10.5464 -2.1805 13.9239
donorgroup*region Autoab Pos 1_H Ins. pos. T1D 2_B 6.3086 2.4077 35 2.62 0.0129 Tukey-Kramer 0.3071 0.05 1.4208 11.1964 -2.1105 14.7278
donorgroup*region Autoab Pos 1_H Ins. pos. T1D 3_T 3.9273 2.4471 35 1.60 0.1175 Tukey-Kramer 0.8958 0.05 -1.0406 8.8952 -4.6299 12.4844
donorgroup*region Autoab Pos 1_H No diabetes 1_H -1.5093 2.1556 35 -0.70 0.4884 Tukey-Kramer 0.9999 0.05 -5.8855 2.8669 -9.0472 6.0286
donorgroup*region Autoab Pos 1_H No diabetes 2_B -1.6083 2.2458 35 -0.72 0.4787 Tukey-Kramer 0.9998 0.05 -6.1675 2.9510 -9.4615 6.2450
donorgroup*region Autoab Pos 1_H No diabetes 3_T -1.1555 2.2664 35 -0.51 0.6134 Tukey-Kramer 1.0000 0.05 -5.7566 3.4456 -9.0808 6.7698
donorgroup*region Autoab Pos 2_B Autoab Pos 3_T 1.3761 1.3712 35 1.00 0.3225 Tukey-Kramer 0.9966 0.05 -1.4076 4.1597 -3.4188 6.1709
donorgroup*region Autoab Pos 2_B Ins. neg. T1D 1_H 1.9415 2.6011 35 0.75 0.4604 Tukey-Kramer 0.9998 0.05 -3.3390 7.2219 -7.1540 11.0370
donorgroup*region Autoab Pos 2_B Ins. neg. T1D 2_B 4.3184 2.7334 35 1.58 0.1231 Tukey-Kramer 0.9050 0.05 -1.2308 9.8675 -5.2400 13.8768
donorgroup*region Autoab Pos 2_B Ins. neg. T1D 3_T 0.4311 2.7830 35 0.15 0.8778 Tukey-Kramer 1.0000 0.05 -5.2188 6.0810 -9.3008 10.1629
donorgroup*region Autoab Pos 2_B Ins. pos. T1D 1_H 6.9004 2.4046 35 2.87 0.0069 Tukey-Kramer 0.1959 0.05 2.0189 11.7819 -1.5080 15.3088
donorgroup*region Autoab Pos 2_B Ins. pos. T1D 2_B 7.3373 2.5052 35 2.93 0.0060 Tukey-Kramer 0.1746 0.05 2.2514 12.4232 -1.4231 16.0978
donorgroup*region Autoab Pos 2_B Ins. pos. T1D 3_T 4.9560 2.5432 35 1.95 0.0594 Tukey-Kramer 0.7222 0.05 -0.2070 10.1189 -3.9371 13.8491
donorgroup*region Autoab Pos 2_B No diabetes 1_H -0.4806 2.2641 35 -0.21 0.8331 Tukey-Kramer 1.0000 0.05 -5.0770 4.1158 -8.3978 7.4366
donorgroup*region Autoab Pos 2_B No diabetes 2_B -0.5796 2.3501 35 -0.25 0.8067 Tukey-Kramer 1.0000 0.05 -5.3506 4.1915 -8.7976 7.6385
donorgroup*region Autoab Pos 2_B No diabetes 3_T -0.1268 2.3698 35 -0.05 0.9576 Tukey-Kramer 1.0000 0.05 -4.9378 4.6842 -8.4137 8.1601
donorgroup*region Autoab Pos 3_T Ins. neg. T1D 1_H 0.5654 2.6467 35 0.21 0.8321 Tukey-Kramer 1.0000 0.05 -4.8077 5.9385 -8.6896 9.8205
donorgroup*region Autoab Pos 3_T Ins. neg. T1D 2_B 2.9423 2.7769 35 1.06 0.2966 Tukey-Kramer 0.9946 0.05 -2.6951 8.5797 -6.7680 12.6526
donorgroup*region Autoab Pos 3_T Ins. neg. T1D 3_T -0.9450 2.8257 35 -0.33 0.7401 Tukey-Kramer 1.0000 0.05 -6.6815 4.7916 -10.8261 8.9361
donorgroup*region Autoab Pos 3_T Ins. pos. T1D 1_H 5.5243 2.4538 35 2.25 0.0307 Tukey-Kramer 0.5266 0.05 0.5428 10.5059 -3.0564 14.1050
donorgroup*region Autoab Pos 3_T Ins. pos. T1D 2_B 5.9613 2.5526 35 2.34 0.0254 Tukey-Kramer 0.4724 0.05 0.7793 11.1433 -2.9647 14.8872
donorgroup*region Autoab Pos 3_T Ins. pos. T1D 3_T 3.5799 2.5898 35 1.38 0.1756 Tukey-Kramer 0.9595 0.05 -1.6777 8.8376 -5.4763 12.6361
donorgroup*region Autoab Pos 3_T No diabetes 1_H -1.8566 2.3164 35 -0.80 0.4282 Tukey-Kramer 0.9995 0.05 -6.5591 2.8459 -9.9566 6.2434
donorgroup*region Autoab Pos 3_T No diabetes 2_B -1.9556 2.4005 35 -0.81 0.4208 Tukey-Kramer 0.9995 0.05 -6.8290 2.9177 -10.3499 6.4387
donorgroup*region Autoab Pos 3_T No diabetes 3_T -1.5028 2.4198 35 -0.62 0.5386 Tukey-Kramer 1.0000 0.05 -6.4153 3.4097 -9.9645 6.9589
donorgroup*region Ins. neg. T1D 1_H Ins. neg. T1D 2_B 2.3769 1.2074 35 1.97 0.0570 Tukey-Kramer 0.7099 0.05 -0.07428 4.8280 -1.8452 6.5990
donorgroup*region Ins. neg. T1D 1_H Ins. neg. T1D 3_T -1.5104 1.5608 35 -0.97 0.3398 Tukey-Kramer 0.9975 0.05 -4.6789 1.6581 -6.9681 3.9473
donorgroup*region Ins. neg. T1D 1_H Ins. pos. T1D 1_H 4.9589 2.3609 35 2.10 0.0430 Tukey-Kramer 0.6257 0.05 0.1660 9.7518 -3.2968 13.2147
donorgroup*region Ins. neg. T1D 1_H Ins. pos. T1D 2_B 5.3959 2.4634 35 2.19 0.0352 Tukey-Kramer 0.5666 0.05 0.3949 10.3968 -3.2182 14.0099
donorgroup*region Ins. neg. T1D 1_H Ins. pos. T1D 3_T 3.0145 2.5020 35 1.20 0.2363 Tukey-Kramer 0.9850 0.05 -2.0647 8.0938 -5.7344 11.7634
donorgroup*region Ins. neg. T1D 1_H No diabetes 1_H -2.4221 2.2177 35 -1.09 0.2822 Tukey-Kramer 0.9931 0.05 -6.9242 2.0801 -10.1770 5.3328
donorgroup*region Ins. neg. T1D 1_H No diabetes 2_B -2.5210 2.3055 35 -1.09 0.2816 Tukey-Kramer 0.9930 0.05 -7.2014 2.1593 -10.5828 5.5408
donorgroup*region Ins. neg. T1D 1_H No diabetes 3_T -2.0682 2.3255 35 -0.89 0.3799 Tukey-Kramer 0.9988 0.05 -6.7893 2.6528 -10.2002 6.0637
donorgroup*region Ins. neg. T1D 2_B Ins. neg. T1D 3_T -3.8873 1.4659 35 -2.65 0.0119 Tukey-Kramer 0.2911 0.05 -6.8632 -0.9114 -9.0132 1.2386
donorgroup*region Ins. neg. T1D 2_B Ins. pos. T1D 1_H 2.5820 2.5060 35 1.03 0.3099 Tukey-Kramer 0.9958 0.05 -2.5054 7.6695 -6.1810 11.3451
donorgroup*region Ins. neg. T1D 2_B Ins. pos. T1D 2_B 3.0190 2.6028 35 1.16 0.2539 Tukey-Kramer 0.9889 0.05 -2.2649 8.3029 -6.0824 12.1204
donorgroup*region Ins. neg. T1D 2_B Ins. pos. T1D 3_T 0.6376 2.6393 35 0.24 0.8105 Tukey-Kramer 1.0000 0.05 -4.7204 5.9957 -8.5916 9.8668
donorgroup*region Ins. neg. T1D 2_B No diabetes 1_H -4.7989 2.3716 35 -2.02 0.0507 Tukey-Kramer 0.6754 0.05 -9.6135 0.01559 -13.0919 3.4940
donorgroup*region Ins. neg. T1D 2_B No diabetes 2_B -4.8979 2.4538 35 -2.00 0.0538 Tukey-Kramer 0.6928 0.05 -9.8795 0.08361 -13.4785 3.6827
donorgroup*region Ins. neg. T1D 2_B No diabetes 3_T -4.4451 2.4727 35 -1.80 0.0809 Tukey-Kramer 0.8084 0.05 -9.4650 0.5747 -13.0917 4.2015
donorgroup*region Ins. neg. T1D 3_T Ins. pos. T1D 1_H 6.4693 2.5600 35 2.53 0.0162 Tukey-Kramer 0.3572 0.05 1.2722 11.6664 -2.4826 15.4213
donorgroup*region Ins. neg. T1D 3_T Ins. pos. T1D 2_B 6.9063 2.6548 35 2.60 0.0135 Tukey-Kramer 0.3168 0.05 1.5167 12.2958 -2.3772 16.1897
donorgroup*region Ins. neg. T1D 3_T Ins. pos. T1D 3_T 4.5249 2.6906 35 1.68 0.1015 Tukey-Kramer 0.8645 0.05 -0.9374 9.9872 -4.8838 13.9336
donorgroup*region Ins. neg. T1D 3_T No diabetes 1_H -0.9117 2.4286 35 -0.38 0.7096 Tukey-Kramer 1.0000 0.05 -5.8419 4.0186 -9.4040 7.5806
donorgroup*region Ins. neg. T1D 3_T No diabetes 2_B -1.0106 2.5090 35 -0.40 0.6895 Tukey-Kramer 1.0000 0.05 -6.1041 4.0828 -9.7841 7.7628
donorgroup*region Ins. neg. T1D 3_T No diabetes 3_T -0.5578 2.5274 35 -0.22 0.8266 Tukey-Kramer 1.0000 0.05 -5.6888 4.5731 -9.3958 8.2801
donorgroup*region Ins. pos. T1D 1_H Ins. pos. T1D 2_B 0.4369 1.0102 35 0.43 0.6680 Tukey-Kramer 1.0000 0.05 -1.6139 2.4877 -3.0955 3.9694
donorgroup*region Ins. pos. T1D 1_H Ins. pos. T1D 3_T -1.9444 1.3058 35 -1.49 0.1454 Tukey-Kramer 0.9339 0.05 -4.5954 0.7066 -6.5107 2.6219
donorgroup*region Ins. pos. T1D 1_H No diabetes 1_H -7.3810 1.9836 35 -3.72 0.0007 Tukey-Kramer 0.0288 0.05 -11.4078 -3.3541 -14.3172 -0.4448
donorgroup*region Ins. pos. T1D 1_H No diabetes 2_B -7.4800 2.0812 35 -3.59 0.0010 Tukey-Kramer 0.0395 0.05 -11.7051 -3.2549 -14.7577 -0.2023
donorgroup*region Ins. pos. T1D 1_H No diabetes 3_T -7.0272 2.1034 35 -3.34 0.0020 Tukey-Kramer 0.0721 0.05 -11.2974 -2.7570 -14.3825 0.3282
donorgroup*region Ins. pos. T1D 2_B Ins. pos. T1D 3_T -2.3813 1.2264 35 -1.94 0.0603 Tukey-Kramer 0.7264 0.05 -4.8711 0.1085 -6.6700 1.9073
donorgroup*region Ins. pos. T1D 2_B No diabetes 1_H -7.8179 2.1045 35 -3.71 0.0007 Tukey-Kramer 0.0292 0.05 -12.0902 -3.5456 -15.1769 -0.4589
donorgroup*region Ins. pos. T1D 2_B No diabetes 2_B -7.9169 2.1968 35 -3.60 0.0010 Tukey-Kramer 0.0386 0.05 -12.3766 -3.4572 -15.5986 -0.2352
donorgroup*region Ins. pos. T1D 2_B No diabetes 3_T -7.4641 2.2178 35 -3.37 0.0019 Tukey-Kramer 0.0681 0.05 -11.9665 -2.9617 -15.2194 0.2912
donorgroup*region Ins. pos. T1D 3_T No diabetes 1_H -5.4366 2.1495 35 -2.53 0.0161 Tukey-Kramer 0.3560 0.05 -9.8003 -1.0728 -12.9530 2.0799
donorgroup*region Ins. pos. T1D 3_T No diabetes 2_B -5.5356 2.2399 35 -2.47 0.0185 Tukey-Kramer 0.3892 0.05 -10.0829 -0.9882 -13.3683 2.2971
donorgroup*region Ins. pos. T1D 3_T No diabetes 3_T -5.0828 2.2606 35 -2.25 0.0309 Tukey-Kramer 0.5285 0.05 -9.6720 -0.4935 -12.9877 2.8221
donorgroup*region No diabetes 1_H No diabetes 2_B -0.09898 0.8791 35 -0.11 0.9110 Tukey-Kramer 1.0000 0.05 -1.8836 1.6857 -3.1730 2.9750
donorgroup*region No diabetes 1_H No diabetes 3_T 0.3538 1.1036 35 0.32 0.7504 Tukey-Kramer 1.0000 0.05 -1.8867 2.5943 -3.5054 4.2130
donorgroup*region No diabetes 2_B No diabetes 3_T 0.4528 1.0575 35 0.43 0.6711 Tukey-Kramer 1.0000 0.05 -1.6940 2.5996 -3.2450 4.1506

figure 2

In [143]:
/*for duct study*/
DATA duct_demo_limited (keep=nPODCaseID Donortype);
    set duct_demo;
RUN;

data duct2;
    merge duct1 (in=a) duct_demo_limited;
    by nPODCaseID;
    if a;
RUN;

DATA duct3;
    set duct2;
    duct_thickness_old=('Main Duct Mean Thickness (um)'n)/('Total Tissue Area (mm^2)'n); /*originally considered, but incorrect*/
    duct_thickness_relative=('Main Duct Mean Thickness (um)'n)/('Main Duct Area (mm^2)'n);
    duct_thickness_absolute='Main Duct Mean Thickness (um)'n;
    percent_duct_area=('Main Duct Area (mm^2)'n)/('Total Tissue Area (mm^2)'n)*100;
    duct_area='Main Duct Area (mm^2)'n;
    donorgroup=donortype;
    if INS=0 and donortype="T1D" then donorgroup="Ins. neg. T1D";
    if INS=1 and donortype="T1D" then donorgroup="Ins. pos. T1D";
RUN;



PROC sql;
    create table duct4 as
    select * from duct3
    outer union corr
    select nPODCaseID, DonorType,donorgroup,
    mean(percent_duct_area) as percent_duct_area,
    'O' as region
    from duct3
    group by nPODCaseID, DonorType,donorgroup
    order by nPODCaseID, DonorType, donorgroup, region;
quit;



/*inspect data*/

proc export data=duct3
     outfile="&location\Data\duct3.csv" 
     dbms=csv
     replace;
run; 


proc export data=duct4
     outfile="&location\Data\duct4.csv" 
     dbms=csv
     replace;
run;
Out[143]:

96                                                         The SAS System                         22:22 Wednesday, November 11, 2020

14487 ods listing close;ods html5 (id=saspy_internal) file=_tomods1 options(bitmap_mode='inline') device=svg style=HTMLBlue;
14487 ! ods graphics on / outputfmt=png;
NOTE: Writing HTML5(SASPY_INTERNAL) Body file: _TOMODS1
14488
14489 /*for duct study*/
14490 DATA duct_demo_limited (keep=nPODCaseID Donortype);
14491 set duct_demo;
14492 RUN;

NOTE: There were 32 observations read from the data set WORK.DUCT_DEMO.
NOTE: The data set WORK.DUCT_DEMO_LIMITED has 32 observations and 2 variables.
NOTE: DATA statement used (Total process time):
real time 0.01 seconds
cpu time 0.01 seconds


14493
14494 data duct2;
14495 merge duct1 (in=a) duct_demo_limited;
14496 by nPODCaseID;
14497 if a;
14498 RUN;

NOTE: There were 96 observations read from the data set WORK.DUCT1.
NOTE: There were 32 observations read from the data set WORK.DUCT_DEMO_LIMITED.
NOTE: The data set WORK.DUCT2 has 96 observations and 9 variables.
NOTE: DATA statement used (Total process time):
real time 0.01 seconds
cpu time 0.01 seconds


14499
14500 DATA duct3;
14501 set duct2;
14502 duct_thickness_old=('Main Duct Mean Thickness (um)'n)/('Total Tissue Area (mm^2)'n); /*originally considered, but
14502 ! incorrect*/
14503 duct_thickness_relative=('Main Duct Mean Thickness (um)'n)/('Main Duct Area (mm^2)'n);
14504 duct_thickness_absolute='Main Duct Mean Thickness (um)'n;
14505 percent_duct_area=('Main Duct Area (mm^2)'n)/('Total Tissue Area (mm^2)'n)*100;
14506 duct_area='Main Duct Area (mm^2)'n;
14507 donorgroup=donortype;
14508 if INS=0 and donortype="T1D" then donorgroup="Ins. neg. T1D";
14509 if INS=1 and donortype="T1D" then donorgroup="Ins. pos. T1D";
14510 RUN;

NOTE: There were 96 observations read from the data set WORK.DUCT2.
NOTE: The data set WORK.DUCT3 has 96 observations and 15 variables.
NOTE: DATA statement used (Total process time):
real time 0.01 seconds
cpu time 0.01 seconds


14511
14512
14513
14514 PROC sql;
14515 create table duct4 as
14516 select * from duct3
14517 outer union corr
14518 select nPODCaseID, DonorType,donorgroup,
14519 mean(percent_duct_area) as percent_duct_area,
14520 'O' as region
14521 from duct3
14522 group by nPODCaseID, DonorType,donorgroup
14523 order by nPODCaseID, DonorType, donorgroup, region;
NOTE: Table WORK.DUCT4 created, with 128 rows and 15 columns.

14524 quit;
NOTE: PROCEDURE SQL used (Total process time):
real time 0.02 seconds
cpu time 0.06 seconds


14525
14526
14527
14528 /*inspect data*/
14529
14530 proc export data=duct3
14531 outfile="&location\Data\duct3.csv"
14532 dbms=csv
14533 replace;
14534 run;

14535 /**********************************************************************
14536 * PRODUCT: SAS
14537 * VERSION: 9.4
14538 * CREATOR: External File Interface
14539 * DATE: 11NOV20
14540 * DESC: Generated SAS Datastep Code
14541 * TEMPLATE SOURCE: (None Specified.)
14542 ***********************************************************************/
14543 data _null_;
14544 %let _EFIERR_ = 0; /* set the ERROR detection macro variable */
14545 %let _EFIREC_ = 0; /* clear export record count macro variable */
14546 file 'C:\Users\jkaddis\Desktop\pancreas_size\Data\duct3.csv' delimiter=',' DSD DROPOVER lrecl=32767;
14547 if _n_ = 1 then /* write column names or labels */
14548 do;
14549 put
14550 "region"
14551 ','
14552 "INS"
14553 ','
14554 "Main Duct Mean Thickness (um)"
14555 ','
14556 "Main Duct Area (mm^2)"
14557 ','
14558 "Total Tissue Area (mm^2)"
14559 ','
14560 "thickness/total tissue area"
14561 ','
14562 "percentage of duct area out of t"
14563 ','
14564 "nPODCaseID"
14565 ','
14566 "DonorType"
14567 ','
14568 "duct_thickness_old"
14569 ','
14570 "duct_thickness_relative"
14571 ','
14572 "duct_thickness_absolute"
14573 ','
14574 "percent_duct_area"
14575 ','
14576 "duct_area"
14577 ','
14578 "donorgroup"
14579 ;
14580 end;
14581 set DUCT3 end=EFIEOD;
14582 format region $7. ;
14583 format INS best10. ;
14584 format "Main Duct Mean Thickness (um)"N best20. ;
14585 format "Main Duct Area (mm^2)"N best20. ;
14586 format "Total Tissue Area (mm^2)"N best20. ;
14587 format "thickness/total tissue area"N best20. ;
14588 format "percentage of duct area out of t"N best20. ;
14589 format nPODCaseID $8. ;
14590 format DonorType $24. ;
14591 format duct_thickness_old best12. ;
14592 format duct_thickness_relative best12. ;
14593 format duct_thickness_absolute best12. ;
14594 format percent_duct_area best12. ;
14595 format duct_area best12. ;
14596 format donorgroup $24. ;
14597 do;
14598 EFIOUT + 1;
14599 put region $ @;
14600 put INS @;
14601 put "Main Duct Mean Thickness (um)"N @;
14602 put "Main Duct Area (mm^2)"N @;
14603 put "Total Tissue Area (mm^2)"N @;
14604 put "thickness/total tissue area"N @;
14605 put "percentage of duct area out of t"N @;
14606 put nPODCaseID $ @;
14607 put DonorType $ @;
14608 put duct_thickness_old @;
14609 put duct_thickness_relative @;
14610 put duct_thickness_absolute @;
14611 put percent_duct_area @;
14612 put duct_area @;
14613 put donorgroup $ ;
14614 ;
14615 end;
14616 if _ERROR_ then call symputx('_EFIERR_',1); /* set ERROR detection macro variable */
14617 if EFIEOD then call symputx('_EFIREC_',EFIOUT);
14618 run;

NOTE: The file 'C:\Users\jkaddis\Desktop\pancreas_size\Data\duct3.csv' is:
Filename=C:\Users\jkaddis\Desktop\pancreas_size\Data\duct3.csv,
RECFM=V,LRECL=32767,File Size (bytes)=0,
Last Modified=12Nov2020:01:21:33,
Create Time=12Nov2020:01:21:33

NOTE: 97 records were written to the file 'C:\Users\jkaddis\Desktop\pancreas_size\Data\duct3.csv'.
The minimum record length was 147.
The maximum record length was 275.
NOTE: There were 96 observations read from the data set WORK.DUCT3.
NOTE: DATA statement used (Total process time):
real time 0.02 seconds
cpu time 0.01 seconds


96 records created in C:\Users\jkaddis\Desktop\pancreas_size\Data\duct3.csv from DUCT3.


NOTE: "C:\Users\jkaddis\Desktop\pancreas_size\Data\duct3.csv" file was successfully created.
NOTE: PROCEDURE EXPORT used (Total process time):
real time 0.05 seconds
cpu time 0.06 seconds


14619
14620
14621 proc export data=duct4
14622 outfile="&location\Data\duct4.csv"
14623 dbms=csv
14624 replace;
14625 run;

14626 /**********************************************************************
14627 * PRODUCT: SAS
14628 * VERSION: 9.4
14629 * CREATOR: External File Interface
14630 * DATE: 11NOV20
14631 * DESC: Generated SAS Datastep Code
14632 * TEMPLATE SOURCE: (None Specified.)
14633 ***********************************************************************/
14634 data _null_;
14635 %let _EFIERR_ = 0; /* set the ERROR detection macro variable */
14636 %let _EFIREC_ = 0; /* clear export record count macro variable */
14637 file 'C:\Users\jkaddis\Desktop\pancreas_size\Data\duct4.csv' delimiter=',' DSD DROPOVER lrecl=32767;
14638 if _n_ = 1 then /* write column names or labels */
14639 do;
14640 put
14641 "region"
14642 ','
14643 "INS"
14644 ','
14645 "Main Duct Mean Thickness (um)"
14646 ','
14647 "Main Duct Area (mm^2)"
14648 ','
14649 "Total Tissue Area (mm^2)"
14650 ','
14651 "thickness/total tissue area"
14652 ','
14653 "percentage of duct area out of t"
14654 ','
14655 "nPODCaseID"
14656 ','
14657 "DonorType"
14658 ','
14659 "duct_thickness_old"
14660 ','
14661 "duct_thickness_relative"
14662 ','
14663 "duct_thickness_absolute"
14664 ','
14665 "percent_duct_area"
14666 ','
14667 "duct_area"
14668 ','
14669 "donorgroup"
14670 ;
14671 end;
14672 set DUCT4 end=EFIEOD;
14673 format region $7. ;
14674 format INS best10. ;
14675 format "Main Duct Mean Thickness (um)"N best20. ;
14676 format "Main Duct Area (mm^2)"N best20. ;
14677 format "Total Tissue Area (mm^2)"N best20. ;
14678 format "thickness/total tissue area"N best20. ;
14679 format "percentage of duct area out of t"N best20. ;
14680 format nPODCaseID $8. ;
14681 format DonorType $24. ;
14682 format duct_thickness_old best12. ;
14683 format duct_thickness_relative best12. ;
14684 format duct_thickness_absolute best12. ;
14685 format percent_duct_area best12. ;
14686 format duct_area best12. ;
14687 format donorgroup $24. ;
14688 do;
14689 EFIOUT + 1;
14690 put region $ @;
14691 put INS @;
14692 put "Main Duct Mean Thickness (um)"N @;
14693 put "Main Duct Area (mm^2)"N @;
14694 put "Total Tissue Area (mm^2)"N @;
14695 put "thickness/total tissue area"N @;
14696 put "percentage of duct area out of t"N @;
14697 put nPODCaseID $ @;
14698 put DonorType $ @;
14699 put duct_thickness_old @;
14700 put duct_thickness_relative @;
14701 put duct_thickness_absolute @;
14702 put percent_duct_area @;
14703 put duct_area @;
14704 put donorgroup $ ;
14705 ;
14706 end;
14707 if _ERROR_ then call symputx('_EFIERR_',1); /* set ERROR detection macro variable */
14708 if EFIEOD then call symputx('_EFIREC_',EFIOUT);
14709 run;

NOTE: The file 'C:\Users\jkaddis\Desktop\pancreas_size\Data\duct4.csv' is:
Filename=C:\Users\jkaddis\Desktop\pancreas_size\Data\duct4.csv,
RECFM=V,LRECL=32767,File Size (bytes)=0,
Last Modified=12Nov2020:01:21:33,
Create Time=12Nov2020:01:21:33

NOTE: 129 records were written to the file 'C:\Users\jkaddis\Desktop\pancreas_size\Data\duct4.csv'.
The minimum record length was 46.
The maximum record length was 275.
NOTE: There were 128 observations read from the data set WORK.DUCT4.
NOTE: DATA statement used (Total process time):
real time 0.02 seconds
cpu time 0.04 seconds


128 records created in C:\Users\jkaddis\Desktop\pancreas_size\Data\duct4.csv from DUCT4.


NOTE: "C:\Users\jkaddis\Desktop\pancreas_size\Data\duct4.csv" file was successfully created.
NOTE: PROCEDURE EXPORT used (Total process time):
real time 0.05 seconds
cpu time 0.07 seconds


14710
14711
14712 ods html5 (id=saspy_internal) close;ods listing;
14713
In [144]:
boxplot<-import("duct3.csv")


boxplot %<>% mutate(donor_range = ifelse(donorgroup == "No diabetes", "No diabetes",
                                              ifelse(donorgroup == "Ins. pos. T1D", "T1D INS+",
                                                    "T1D INS-")))

boxplot <- within(boxplot,donor_range <- factor(donor_range,
                                            levels=rev(c("T1D INS-",
                                                     "T1D INS+",
                                                           "No diabetes"))))


boxplot %<>% mutate(region = ifelse(region == "PH", "Head",
                                             ifelse(region == "PB", "Body",
                                                    "Tail")))

# for reordering the columns
boxplot <- within(boxplot,region <- factor(region,
                                            levels=rev(c("Tail",
                                                     "Body",
                                                     "Head"))))




#boxplots defaults used, i.e. box represents IQR, whiskers 1.5*IQR, beyond whiskers are outliers, and line within box is the median.  
fig8<-ggplot(boxplot, aes(region,duct_area)) +
geom_boxplot(outlier.size=NA, outlier.color=NA, color="black", alpha=0.3, show.legend=FALSE, color=boxplot$donor_range) +
scale_color_manual(guide = FALSE, values =c("#1B9E77", "#7570B3", "#E7298A")) + #comment this line out if you want to use R's auto-color palette
scale_fill_manual(guide = FALSE, values=c("No diabetes" = "#1B9E77", "T1D INS+" = "#7570B3", "T1D INS-" = "#E7298A")) +  #comment this line out if you want to use R's auto-color palette
  

geom_jitter(aes(region,duct_area, color=boxplot$donor_range),
        position=position_jitter(width=0.3,height=0),
        alpha=0.5,
        size=3,
        show.legend=FALSE)+
    xlab("Pancreas Region") +
    ylab("Main Duct Area \n(mm²)") +
    theme(axis.title = element_text(size=20,color='black', family="Arial", face="bold"),
          axis.text = element_text(size=20,color='black', family="Arial"), 
          axis.ticks=element_line(color="black"),
          panel.background=element_blank())+
     panel_border(colour = "black", size = 0.5, linetype = 1, remove = FALSE)+
     geom_signif(y_position=3.5, xmin=2, xmax=3,
     annotation="*", tip_length=0, size=1, textsize=8, color="black") + #see here https://rdrr.io/cran/ggsignif/man/stat_signif.html

scale_y_continuous(limits=c(0,4))

fig8

save_plot("fig1_part2.tiff", fig8, base_aspect_ratio=1/1.05)
Warning message:
"Duplicated aesthetics after name standardisation: colour"
Warning message:
"Use of `boxplot$donor_range` is discouraged. Use `donor_range` instead."
Warning message in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
"font family not found in Windows font database"
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"font family not found in Windows font database"
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"font family not found in Windows font database"
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"font family not found in Windows font database"
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"font family not found in Windows font database"
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"font family not found in Windows font database"
Warning message:
"Use of `boxplot$donor_range` is discouraged. Use `donor_range` instead."
Warning message in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
"font family not found in Windows font database"
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"font family not found in Windows font database"
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In [145]:
#try alternative version of above figure

my_data<-import("duct3.csv")





#Recode and order the variables
my_data %<>% mutate(donor_range = ifelse(donorgroup == "No diabetes", "No T1D",
                                       ifelse(donorgroup == "Autoab Pos", "AAb+",
                                              ifelse(donorgroup == "Ins. pos. T1D", "T1D I+",
                                                    "T1D I-"))))

my_data <- within(my_data,donor_range <- factor(donor_range,
                                            levels=rev(c("T1D I-",
                                                     "T1D I+",
                                                     "AAb+",
                                                        "No T1D"))))


#Recode and order the variables
my_data %<>% mutate(region = ifelse(region == "PH", "Head",
                                             ifelse(region == "PB", "Body",
                                                    "Tail")))

my_data <- within(my_data,region <- factor(region,
                                            levels=rev(c("Tail",
                                                     "Body",
                                                     "Head"))))



#boxplots defaults used, i.e. box represents IQR, whiskers 1.5*IQR, beyond whiskers are outliers, and line within box is the median.  
fig8<-ggplot(my_data, aes(region,duct_thickness_absolute)) +
geom_boxplot(outlier.size=NA, outlier.color=NA, color="black", alpha=0.3, show.legend=FALSE, color=my_data$donor_range) +
scale_color_manual(guide = FALSE, values =c("#1B9E77", "#7570B3", "#E7298A")) + #comment this line out if you want to use R's auto-color palette
scale_fill_manual(guide = FALSE, values=c("No diabetes" = "#1B9E77", "T1D INS+" = "#7570B3", "T1D INS-" = "#E7298A")) +  #comment this line out if you want to use R's auto-color palette
  

geom_jitter(aes(region,duct_thickness_absolute, color=my_data$donor_range),
        position=position_jitter(width=0.3,height=0),
        alpha=0.5,
        size=3,
        show.legend=FALSE)+
    xlab("Pancreas region") +
    ylab("Main duct wall\nthickness (µm)") +
    theme(axis.title = element_text(size=20,color='black', family="Arial", face="bold"),
          axis.text = element_text(size=20,color='black', family="Arial"), 
          axis.ticks=element_line(color="black"),
          panel.background=element_blank())+
     panel_border(colour = "black", size = 0.5, linetype = 1, remove = FALSE)+
       geom_signif(y_position=c(650), xmin=c(2), xmax=c(3),
              annotation=c("*"), tip_length=0, size=1, color="black", textsize=8, alpha=1)+ #see here https://rdrr.io/cran/ggsignif/man/stat_signif.html
scale_y_continuous(limits=c(0,700))


fig8

save_plot("fig1_part3_version2.tiff", fig8, base_aspect_ratio=1/1.05)
Warning message:
"Duplicated aesthetics after name standardisation: colour"
Warning message:
"Use of `my_data$donor_range` is discouraged. Use `donor_range` instead."
Warning message in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
"font family not found in Windows font database"
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"font family not found in Windows font database"
Warning message:
"Use of `my_data$donor_range` is discouraged. Use `donor_range` instead."
Warning message in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, :
"font family not found in Windows font database"
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In [146]:
head(my_data)
A data.frame: 6 × 16
regionINSMain Duct Mean Thickness (um)Main Duct Area (mm^2)Total Tissue Area (mm^2)thickness/total tissue areapercentage of duct area out of tnPODCaseIDDonorTypeduct_thickness_oldduct_thickness_relativeduct_thickness_absolutepercent_duct_areaduct_areadonorgroupdonor_range
<fct><int><dbl><dbl><dbl><dbl><dbl><int><chr><dbl><dbl><dbl><dbl><dbl><chr><fct>
1Head1296.07311.1194240 40.695547.2753212.75072936052T1D7.275321264.4870296.07312.75072931.1194240Ins. pos. T1DT1D I+
2Body1241.89540.7346199 68.442473.5342881.07333936052T1D3.534288329.2796241.89541.07333930.7346199Ins. pos. T1DT1D I+
3Tail1181.59420.3695368 34.113005.3233121.08327246052T1D5.323312491.4103181.59421.08327240.3695368Ins. pos. T1DT1D I+
4Head0249.51250.5618954 79.184523.1510260.70960276062T1D3.151026444.0550249.51250.70960270.5618954Ins. neg. T1DT1D I-
5Body0362.20541.3265906107.868353.3578471.22982376062T1D3.357847273.0348362.20541.22982371.3265906Ins. neg. T1DT1D I-
6Tail0294.86000.7241359102.344942.8810410.70754456062T1D2.881041407.1887294.86000.70754450.7241359Ins. neg. T1DT1D I-

statistical analysis for figure 2

In [147]:
/*
Covariance structures considered include:
homogeneous covariance structures
vc - simplist, correlation of errors assumed to be 0
cs - compound symmetry, constant variance and covariance

heterogeneous covariance structure
un - unstructured, most complex
unr- unstructured correlation
un(1) - banded main diagonal
csh - heterogeneous compound symmetry
hf - Huynh-Feldt (similar to csh) 
arh(1) - autoregressive heterogeneous
*/


%macro explore (a);

PROC mixed data=duct3 /*maxiter=1000 maxfunc=5000  can also use covtest*/;
     class nPODCaseID donorgroup region;
     model  &a= region|donorgroup/solution; /*can use  ddfm = kenwardroger after solution for unbalanced data to improve performance of t and f tests*/
     /*option e3 after solution helps to describe how type 3 tests were constructed*/
     repeated  region/ subject=nPODCaseID(donorgroup)  type=vc; 
     ods output FitStatistics=Fitvc(rename=(value=vc)) Dimensions=Parmvc(rename=(value=Numvc)) ConvergenceStatus=ConvergeStatusvc; 
     /*lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;*/
run;
DATA ConvergeStatusvc;
    set ConvergeStatusvc;
    covar="vc ";
RUN;

PROC mixed data=duct3 /*maxiter=1000 maxfunc=5000  can also use covtest*/;
     class nPODCaseID donorgroup region;
     model  &a= region|donorgroup/solution; /*can use  ddfm = kenwardroger after solution for unbalanced data to improve performance of t and f tests*/
     /*option e3 after solution helps to describe how type 3 tests were constructed*/
     repeated  region/ subject=nPODCaseID(donorgroup)   type=cs; 
     ods output FitStatistics=Fitcs(rename=(value=cs)) Dimensions=Parmcs(rename=(value=Numcs)) ConvergenceStatus=ConvergeStatuscs;  
     /*lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;*/
run;
DATA ConvergeStatuscs;
    set ConvergeStatuscs;
    covar="cs ";
RUN;

PROC mixed data=duct3 /*maxiter=1000 maxfunc=5000  can also use covtest*/;
     class nPODCaseID donorgroup region;
     model  &a= region|donorgroup/solution;/*can use  ddfm = kenwardroger after solution for unbalanced data to improve performance of t and f tests*/
     /*option e3 after solution helps to describe how type 3 tests were constructed*/
     repeated  region/ subject=nPODCaseID(donorgroup)   type=un; 
     ods output FitStatistics=Fitun(rename=(value=un)) Dimensions=Parmun(rename=(value=Numun)) ConvergenceStatus=ConvergeStatusun;  
     /*lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;*/
run;
DATA ConvergeStatusun;
    set ConvergeStatusun;
    covar="un ";
RUN;

PROC mixed data=duct3 /*maxiter=1000 maxfunc=5000  can also use covtest*/;
     class nPODCaseID donorgroup region;
     model  &a= region|donorgroup/solution; /*can use  ddfm = kenwardroger after solution for unbalanced data to improve performance of t and f tests*/
     /*option e3 after solution helps to describe how type 3 tests were constructed*/
     repeated  region/ subject=nPODCaseID(donorgroup)   type=unr; 
     ods output FitStatistics=Fitunr(rename=(value=unr)) Dimensions=Parmunr(rename=(value=Numunr)) ConvergenceStatus=ConvergeStatusunr;  
     /*lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;*/
run;
DATA ConvergeStatusunr;
    set ConvergeStatusunr;
    covar="unr";
RUN;

PROC mixed data=duct3 /*maxiter=1000 maxfunc=5000  can also use covtest*/;
     class nPODCaseID donorgroup region;
     model  &a= region|donorgroup/solution; /*can use  ddfm = kenwardroger after solution for unbalanced data to improve performance of t and f tests*/
     /*option e3 after solution helps to describe how type 3 tests were constructed*/
     repeated  region/ subject=nPODCaseID(donorgroup)  type=un(1); 
     ods output FitStatistics=Fitun1(rename=(value=un1)) Dimensions=Parmun1(rename=(value=Numun1)) ConvergenceStatus=ConvergeStatusun1;  
     parms/ols;
     /*lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;*/
run;
DATA ConvergeStatusun1;
    set ConvergeStatusun1;
    covar="un1";
RUN;

PROC mixed data=duct3 /*maxiter=1000 maxfunc=5000  can also use covtest*/;
     class nPODCaseID donorgroup region;
     model  &a= region|donorgroup/solution; /*can use  ddfm = kenwardroger after solution for unbalanced data to improve performance of t and f tests*/
     /*option e3 after solution helps to describe how type 3 tests were constructed*/
     repeated  region/ subject=nPODCaseID(donorgroup)  type=csh; 
     ods output FitStatistics=Fitcsh(rename=(value=csh)) Dimensions=Parmcsh(rename=(value=Numcsh)) ConvergenceStatus=ConvergeStatuscsh; 
     /*lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;*/
run;
DATA ConvergeStatuscsh;
    set ConvergeStatuscsh;
    covar="csh";
RUN;

PROC mixed data=duct3 /*maxiter=1000 maxfunc=5000  can also use covtest*/;
     class nPODCaseID donorgroup region;
     model  &a= region|donorgroup/solution; /*can use  ddfm = kenwardroger after solution for unbalanced data to improve performance of t and f tests*/
     /*option e3 after solution helps to describe how type 3 tests were constructed*/
     repeated  region/ subject=nPODCaseID(donorgroup)  type=hf; 
     ods output FitStatistics=Fithf(rename=(value=hf)) Dimensions=Parmhf(rename=(value=Numhf)) ConvergenceStatus=ConvergeStatushf;
     /*lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;*/
run;
DATA ConvergeStatushf;
    set ConvergeStatushf;
    covar="hf ";
RUN;

PROC mixed data=duct3 /*maxiter=1000 maxfunc=5000  can also use covtest*/;
     class nPODCaseID donorgroup region;
     model  &a= region|donorgroup/solution; /*can use  ddfm = kenwardroger after solution for unbalanced data to improve performance of t and f tests*/
     /*option e3 after solution helps to describe how type 3 tests were constructed*/
     repeated  region/ subject=nPODCaseID(donorgroup)  type=arh(1); 
     ods output FitStatistics=Fitarh1(rename=(value=arh1)) Dimensions=Parmarh1(rename=(value=Numarh1)) ConvergenceStatus=ConvergeStatusarh1;
     /*lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;*/
run;
DATA ConvergeStatusarh1;
    set ConvergeStatusarh1;
    covar="arh(1) ";
RUN;

DATA all;
    merge work.fit:;
RUN;

/*above merge line merges all files with the prefix fit.  The reason for this instead of spelling out each file is because 
some fitstatistics files do not exist for each covar structure tested*/

PROC print data=all label noobs;
RUN;

DATA STATUS;
    set ConvergeStatus:;
RUN;

proc print data=status; run;

%mend explore;
Out[147]:

97                                                         The SAS System                         22:22 Wednesday, November 11, 2020

14716 ods listing close;ods html5 (id=saspy_internal) file=_tomods1 options(bitmap_mode='inline') device=svg style=HTMLBlue;
14716 ! ods graphics on / outputfmt=png;
NOTE: Writing HTML5(SASPY_INTERNAL) Body file: _TOMODS1
14717
14718 /*
14719 Covariance structures considered include:
14720 homogeneous covariance structures
14721 vc - simplist, correlation of errors assumed to be 0
14722 cs - compound symmetry, constant variance and covariance
14723
14724 heterogeneous covariance structure
14725 un - unstructured, most complex
14726 unr- unstructured correlation
14727 un(1) - banded main diagonal
14728 csh - heterogeneous compound symmetry
14729 hf - Huynh-Feldt (similar to csh)
14730 arh(1) - autoregressive heterogeneous
14731 */
14732
14733
14734 %macro explore (a);
14735
14736 PROC mixed data=duct3 /*maxiter=1000 maxfunc=5000 can also use covtest*/;
14737 class nPODCaseID donorgroup region;
14738 model &a= region|donorgroup/solution; /*can use ddfm = kenwardroger after solution for unbalanced data to improve
14738 ! performance of t and f tests*/
14739 /*option e3 after solution helps to describe how type 3 tests were constructed*/
14740 repeated region/ subject=nPODCaseID(donorgroup) type=vc;
14741 ods output FitStatistics=Fitvc(rename=(value=vc)) Dimensions=Parmvc(rename=(value=Numvc))
14741 ! ConvergenceStatus=ConvergeStatusvc;
14742 /*lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;*/
14743 run;
14744 DATA ConvergeStatusvc;
14745 set ConvergeStatusvc;
14746 covar="vc ";
14747 RUN;
14748
14749 PROC mixed data=duct3 /*maxiter=1000 maxfunc=5000 can also use covtest*/;
14750 class nPODCaseID donorgroup region;
14751 model &a= region|donorgroup/solution; /*can use ddfm = kenwardroger after solution for unbalanced data to improve
14751 ! performance of t and f tests*/
14752 /*option e3 after solution helps to describe how type 3 tests were constructed*/
14753 repeated region/ subject=nPODCaseID(donorgroup) type=cs;
14754 ods output FitStatistics=Fitcs(rename=(value=cs)) Dimensions=Parmcs(rename=(value=Numcs))
14754 ! ConvergenceStatus=ConvergeStatuscs;
14755 /*lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;*/
14756 run;
14757 DATA ConvergeStatuscs;
14758 set ConvergeStatuscs;
14759 covar="cs ";
14760 RUN;
14761
14762 PROC mixed data=duct3 /*maxiter=1000 maxfunc=5000 can also use covtest*/;
14763 class nPODCaseID donorgroup region;
14764 model &a= region|donorgroup/solution;/*can use ddfm = kenwardroger after solution for unbalanced data to improve
14764 ! performance of t and f tests*/
14765 /*option e3 after solution helps to describe how type 3 tests were constructed*/
14766 repeated region/ subject=nPODCaseID(donorgroup) type=un;
14767 ods output FitStatistics=Fitun(rename=(value=un)) Dimensions=Parmun(rename=(value=Numun))
14767 ! ConvergenceStatus=ConvergeStatusun;
14768 /*lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;*/
14769 run;
14770 DATA ConvergeStatusun;
14771 set ConvergeStatusun;
14772 covar="un ";
14773 RUN;
14774
14775 PROC mixed data=duct3 /*maxiter=1000 maxfunc=5000 can also use covtest*/;
14776 class nPODCaseID donorgroup region;
14777 model &a= region|donorgroup/solution; /*can use ddfm = kenwardroger after solution for unbalanced data to improve
14777 ! performance of t and f tests*/
14778 /*option e3 after solution helps to describe how type 3 tests were constructed*/
14779 repeated region/ subject=nPODCaseID(donorgroup) type=unr;
14780 ods output FitStatistics=Fitunr(rename=(value=unr)) Dimensions=Parmunr(rename=(value=Numunr))
14780 ! ConvergenceStatus=ConvergeStatusunr;
14781 /*lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;*/
14782 run;
14783 DATA ConvergeStatusunr;
14784 set ConvergeStatusunr;
14785 covar="unr";
14786 RUN;
14787
14788 PROC mixed data=duct3 /*maxiter=1000 maxfunc=5000 can also use covtest*/;
14789 class nPODCaseID donorgroup region;
14790 model &a= region|donorgroup/solution; /*can use ddfm = kenwardroger after solution for unbalanced data to improve
14790 ! performance of t and f tests*/
14791 /*option e3 after solution helps to describe how type 3 tests were constructed*/
14792 repeated region/ subject=nPODCaseID(donorgroup) type=un(1);
14793 ods output FitStatistics=Fitun1(rename=(value=un1)) Dimensions=Parmun1(rename=(value=Numun1))
14793 ! ConvergenceStatus=ConvergeStatusun1;
14794 parms/ols;
14795 /*lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;*/
14796 run;
14797 DATA ConvergeStatusun1;
14798 set ConvergeStatusun1;
14799 covar="un1";
14800 RUN;
14801
14802 PROC mixed data=duct3 /*maxiter=1000 maxfunc=5000 can also use covtest*/;
14803 class nPODCaseID donorgroup region;
14804 model &a= region|donorgroup/solution; /*can use ddfm = kenwardroger after solution for unbalanced data to improve
14804 ! performance of t and f tests*/
14805 /*option e3 after solution helps to describe how type 3 tests were constructed*/
14806 repeated region/ subject=nPODCaseID(donorgroup) type=csh;
14807 ods output FitStatistics=Fitcsh(rename=(value=csh)) Dimensions=Parmcsh(rename=(value=Numcsh))
14807 ! ConvergenceStatus=ConvergeStatuscsh;
14808 /*lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;*/
14809 run;
14810 DATA ConvergeStatuscsh;
14811 set ConvergeStatuscsh;
14812 covar="csh";
14813 RUN;
14814
14815 PROC mixed data=duct3 /*maxiter=1000 maxfunc=5000 can also use covtest*/;
14816 class nPODCaseID donorgroup region;
14817 model &a= region|donorgroup/solution; /*can use ddfm = kenwardroger after solution for unbalanced data to improve
14817 ! performance of t and f tests*/
14818 /*option e3 after solution helps to describe how type 3 tests were constructed*/
14819 repeated region/ subject=nPODCaseID(donorgroup) type=hf;
14820 ods output FitStatistics=Fithf(rename=(value=hf)) Dimensions=Parmhf(rename=(value=Numhf))
14820 ! ConvergenceStatus=ConvergeStatushf;
14821 /*lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;*/
14822 run;
14823 DATA ConvergeStatushf;
14824 set ConvergeStatushf;
14825 covar="hf ";
14826 RUN;
14827
14828 PROC mixed data=duct3 /*maxiter=1000 maxfunc=5000 can also use covtest*/;
14829 class nPODCaseID donorgroup region;
14830 model &a= region|donorgroup/solution; /*can use ddfm = kenwardroger after solution for unbalanced data to improve
14830 ! performance of t and f tests*/
14831 /*option e3 after solution helps to describe how type 3 tests were constructed*/
14832 repeated region/ subject=nPODCaseID(donorgroup) type=arh(1);
14833 ods output FitStatistics=Fitarh1(rename=(value=arh1)) Dimensions=Parmarh1(rename=(value=Numarh1))
14833 ! ConvergenceStatus=ConvergeStatusarh1;
14834 /*lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;*/
14835 run;
14836 DATA ConvergeStatusarh1;
14837 set ConvergeStatusarh1;
14838 covar="arh(1) ";
14839 RUN;
14840
14841 DATA all;
14842 merge work.fit:;
14843 RUN;
14844
14845 /*above merge line merges all files with the prefix fit. The reason for this instead of spelling out each file is
14845 ! because
14846 some fitstatistics files do not exist for each covar structure tested*/
14847
14848 PROC print data=all label noobs;
14849 RUN;
14850
14851 DATA STATUS;
14852 set ConvergeStatus:;
14853 RUN;
14854
14855 proc print data=status; run;
14856
14857 %mend explore;
14858
14859
14860
14861 ods html5 (id=saspy_internal) close;ods listing;
14862
In [148]:
%explore(duct_thickness_absolute);
Out[148]:
SAS Output

SAS Output

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.DUCT3
Dependent Variable duct_thickness_absolute
Covariance Structure Variance Components
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method Parameter
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 32 6052 6062 6079 6087 6195 6209 6228 6233 6238 6243 6247 6265 6278 6293 6318 6334 6339 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6434 6445 6471 6472
donorgroup 3 Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 1
Columns in X 16
Columns in Z 0
Subjects 32
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 96
Number of Observations Used 96
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 1005.09231733  
1 1 1005.09231733 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
region nPODCaseI(donorgrou) 4845.53

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 1005.1
AIC (Smaller is Better) 1007.1
AICC (Smaller is Better) 1007.1
BIC (Smaller is Better) 1008.6

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
0 0.00 1.0000

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     259.67 17.4025 29 14.92 <.0001
region   PB 56.1677 24.6108 58 2.28 0.0262
region   PH 36.5530 24.6108 58 1.49 0.1429
region   PT 0 . . . .
donorgroup Ins. neg. T1D   -1.9525 38.9131 29 -0.05 0.9603
donorgroup Ins. pos. T1D   -4.6861 26.5827 29 -0.18 0.8613
donorgroup No diabetes   0 . . . .
donorgroup*region Ins. neg. T1D PB -11.1702 55.0314 58 -0.20 0.8399
donorgroup*region Ins. neg. T1D PH -9.6170 55.0314 58 -0.17 0.8619
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 6.3865 37.5936 58 0.17 0.8657
donorgroup*region Ins. pos. T1D PH 34.2323 37.5936 58 0.91 0.3663
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 58 3.97 0.0242
donorgroup 2 29 0.34 0.7142
donorgroup*region 4 58 0.29 0.8846

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.DUCT3
Dependent Variable duct_thickness_absolute
Covariance Structure Compound Symmetry
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method Profile
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 32 6052 6062 6079 6087 6195 6209 6228 6233 6238 6243 6247 6265 6278 6293 6318 6334 6339 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6434 6445 6471 6472
donorgroup 3 Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 2
Columns in X 16
Columns in Z 0
Subjects 32
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 96
Number of Observations Used 96
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 1005.09231733  
1 1 997.74710130 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
CS nPODCaseI(donorgrou) 1483.30
Residual   3362.23

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 997.7
AIC (Smaller is Better) 1001.7
AICC (Smaller is Better) 1001.9
BIC (Smaller is Better) 1004.7

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
1 7.35 0.0067

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     259.67 17.4025 29 14.92 <.0001
region   PB 56.1677 20.5007 58 2.74 0.0082
region   PH 36.5530 20.5007 58 1.78 0.0798
region   PT 0 . . . .
donorgroup Ins. neg. T1D   -1.9525 38.9131 29 -0.05 0.9603
donorgroup Ins. pos. T1D   -4.6861 26.5827 29 -0.18 0.8613
donorgroup No diabetes   0 . . . .
donorgroup*region Ins. neg. T1D PB -11.1702 45.8410 58 -0.24 0.8083
donorgroup*region Ins. neg. T1D PH -9.6170 45.8410 58 -0.21 0.8346
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 6.3865 31.3153 58 0.20 0.8391
donorgroup*region Ins. pos. T1D PH 34.2323 31.3153 58 1.09 0.2788
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 58 5.72 0.0054
donorgroup 2 29 0.21 0.8109
donorgroup*region 4 58 0.42 0.7970

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.DUCT3
Dependent Variable duct_thickness_absolute
Covariance Structure Unstructured
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 32 6052 6062 6079 6087 6195 6209 6228 6233 6238 6243 6247 6265 6278 6293 6318 6334 6339 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6434 6445 6471 6472
donorgroup 3 Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 6
Columns in X 16
Columns in Z 0
Subjects 32
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 96
Number of Observations Used 96
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 1005.09231733  
1 1 984.57693375 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
UN(1,1) nPODCaseI(donorgrou) 5098.70
UN(2,1) nPODCaseI(donorgrou) 758.47
UN(2,2) nPODCaseI(donorgrou) 6039.81
UN(3,1) nPODCaseI(donorgrou) 2762.97
UN(3,2) nPODCaseI(donorgrou) 928.46
UN(3,3) nPODCaseI(donorgrou) 3398.08

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 984.6
AIC (Smaller is Better) 996.6
AICC (Smaller is Better) 997.6
BIC (Smaller is Better) 1005.4

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
5 20.52 0.0010

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     259.67 14.5733 29 17.82 <.0001
region   PB 56.1677 13.6264 29 4.12 0.0003
region   PH 36.5530 21.7672 29 1.68 0.1038
region   PT 0 . . . .
donorgroup Ins. neg. T1D   -1.9525 32.5868 29 -0.06 0.9526
donorgroup Ins. pos. T1D   -4.6861 22.2610 29 -0.21 0.8347
donorgroup No diabetes   0 . . . .
donorgroup*region Ins. neg. T1D PB -11.1702 30.4695 29 -0.37 0.7166
donorgroup*region Ins. neg. T1D PH -9.6170 48.6729 29 -0.20 0.8447
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 6.3865 20.8146 29 0.31 0.7612
donorgroup*region Ins. pos. T1D PH 34.2323 33.2499 29 1.03 0.3117
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 29 13.38 <.0001
donorgroup 2 29 0.21 0.8109
donorgroup*region 4 29 0.39 0.8143

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.DUCT3
Dependent Variable duct_thickness_absolute
Covariance Structure Unstructured using Correlations
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 32 6052 6062 6079 6087 6195 6209 6228 6233 6238 6243 6247 6265 6278 6293 6318 6334 6339 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6434 6445 6471 6472
donorgroup 3 Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 6
Columns in X 16
Columns in Z 0
Subjects 32
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 96
Number of Observations Used 96
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 1005.09231733  
1 1 984.57693375 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 5098.70
Var(2) nPODCaseI(donorgrou) 6039.81
Var(3) nPODCaseI(donorgrou) 3398.08
Corr(2,1) nPODCaseI(donorgrou) 0.1367
Corr(3,1) nPODCaseI(donorgrou) 0.6638
Corr(3,2) nPODCaseI(donorgrou) 0.2049

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 984.6
AIC (Smaller is Better) 996.6
AICC (Smaller is Better) 997.6
BIC (Smaller is Better) 1005.4

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
5 20.52 0.0010

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     259.67 14.5733 29 17.82 <.0001
region   PB 56.1677 13.6264 29 4.12 0.0003
region   PH 36.5530 21.7672 29 1.68 0.1038
region   PT 0 . . . .
donorgroup Ins. neg. T1D   -1.9525 32.5868 29 -0.06 0.9526
donorgroup Ins. pos. T1D   -4.6861 22.2610 29 -0.21 0.8347
donorgroup No diabetes   0 . . . .
donorgroup*region Ins. neg. T1D PB -11.1702 30.4695 29 -0.37 0.7166
donorgroup*region Ins. neg. T1D PH -9.6170 48.6729 29 -0.20 0.8447
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 6.3865 20.8146 29 0.31 0.7612
donorgroup*region Ins. pos. T1D PH 34.2323 33.2499 29 1.03 0.3117
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 29 13.38 <.0001
donorgroup 2 29 0.21 0.8109
donorgroup*region 4 29 0.39 0.8143

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.DUCT3
Dependent Variable duct_thickness_absolute
Covariance Structure Banded
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 32 6052 6062 6079 6087 6195 6209 6228 6233 6238 6243 6247 6265 6278 6293 6318 6334 6339 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6434 6445 6471 6472
donorgroup 3 Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 6
Columns in X 16
Columns in Z 0
Subjects 32
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 96
Number of Observations Used 96
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 45 1005.09231733  
1 44 421740.97168000 0.49982159
2 44 421740.97167997 0.49982159

Convergence Status

WARNING: Stopped because of too many likelihood evaluations.

Covariance Parameter Values At Last Iteration

Covariance Parameter Values At Last Iteration
Cov Parm Subject Estimate
UN(1,1) nPODCaseI(donorgrou) 1.0000
UN(2,1) nPODCaseI(donorgrou) 0
UN(2,2) nPODCaseI(donorgrou) 1.0000
UN(3,1) nPODCaseI(donorgrou) 0
UN(3,2) nPODCaseI(donorgrou) 0
UN(3,3) nPODCaseI(donorgrou) 1.0000

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.DUCT3
Dependent Variable duct_thickness_absolute
Covariance Structure Heterogeneous Compound Symmetry
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 32 6052 6062 6079 6087 6195 6209 6228 6233 6238 6243 6247 6265 6278 6293 6318 6334 6339 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6434 6445 6471 6472
donorgroup 3 Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 4
Columns in X 16
Columns in Z 0
Subjects 32
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 96
Number of Observations Used 96
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 1005.09231733  
1 2 993.67575227 0.00001068
2 1 993.67123304 0.00000001

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 4920.48
Var(2) nPODCaseI(donorgrou) 6631.39
Var(3) nPODCaseI(donorgrou) 3224.94
CSH nPODCaseI(donorgrou) 0.3423

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 993.7
AIC (Smaller is Better) 1001.7
AICC (Smaller is Better) 1002.2
BIC (Smaller is Better) 1007.5

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
3 11.42 0.0097

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     259.67 14.1971 29 18.29 <.0001
region   PB 56.1677 18.4028 58 3.05 0.0034
region   PH 36.5530 20.4493 58 1.79 0.0791
region   PT 0 . . . .
donorgroup Ins. neg. T1D   -1.9525 31.7458 29 -0.06 0.9514
donorgroup Ins. pos. T1D   -4.6861 21.6865 29 -0.22 0.8304
donorgroup No diabetes   0 . . . .
donorgroup*region Ins. neg. T1D PB -11.1702 41.1499 58 -0.27 0.7870
donorgroup*region Ins. neg. T1D PH -9.6170 45.7259 58 -0.21 0.8342
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 6.3865 28.1108 58 0.23 0.8211
donorgroup*region Ins. pos. T1D PH 34.2323 31.2368 58 1.10 0.2777
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 58 7.22 0.0016
donorgroup 2 29 0.20 0.8187
donorgroup*region 4 58 0.39 0.8128

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.DUCT3
Dependent Variable duct_thickness_absolute
Covariance Structure Huynh-Feldt
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 32 6052 6062 6079 6087 6195 6209 6228 6233 6238 6243 6247 6265 6278 6293 6318 6334 6339 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6434 6445 6471 6472
donorgroup 3 Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 4
Columns in X 16
Columns in Z 0
Subjects 32
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 96
Number of Observations Used 96
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 1005.09231733  
1 2 996.77049680 0.00009637
2 1 996.72788417 0.00000090
3 1 996.72750592 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 6106.06
Var(2) nPODCaseI(donorgrou) 5088.38
Var(3) nPODCaseI(donorgrou) 3714.51
HF nPODCaseI(donorgrou) 3362.22

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 996.7
AIC (Smaller is Better) 1004.7
AICC (Smaller is Better) 1005.2
BIC (Smaller is Better) 1010.6

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
3 8.36 0.0390

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     259.67 15.2367 29 17.04 <.0001
region   PB 56.1677 20.5007 58 2.74 0.0082
region   PH 36.5530 20.5007 58 1.78 0.0798
region   PT 0 . . . .
donorgroup Ins. neg. T1D   -1.9525 34.0703 29 -0.06 0.9547
donorgroup Ins. pos. T1D   -4.6861 23.2744 29 -0.20 0.8418
donorgroup No diabetes   0 . . . .
donorgroup*region Ins. neg. T1D PB -11.1702 45.8409 58 -0.24 0.8083
donorgroup*region Ins. neg. T1D PH -9.6170 45.8409 58 -0.21 0.8346
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 6.3865 31.3153 58 0.20 0.8391
donorgroup*region Ins. pos. T1D PH 34.2323 31.3153 58 1.09 0.2788
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 58 5.72 0.0054
donorgroup 2 29 0.20 0.8186
donorgroup*region 4 58 0.42 0.7970

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.DUCT3
Dependent Variable duct_thickness_absolute
Covariance Structure Heterogeneous Autoregressive
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 32 6052 6062 6079 6087 6195 6209 6228 6233 6238 6243 6247 6265 6278 6293 6318 6334 6339 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6434 6445 6471 6472
donorgroup 3 Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 4
Columns in X 16
Columns in Z 0
Subjects 32
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 96
Number of Observations Used 96
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 1005.09231733  
1 2 1000.94943542 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 5128.28
Var(2) nPODCaseI(donorgrou) 6039.06
Var(3) nPODCaseI(donorgrou) 3377.69
ARH(1) nPODCaseI(donorgrou) 0.1710

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 1000.9
AIC (Smaller is Better) 1008.9
AICC (Smaller is Better) 1009.4
BIC (Smaller is Better) 1014.8

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
3 4.14 0.2464

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     259.67 14.5295 29 17.87 <.0001
region   PB 56.1677 22.7248 58 2.47 0.0164
region   PH 36.5530 22.1817 58 1.65 0.1048
region   PT 0 . . . .
donorgroup Ins. neg. T1D   -1.9525 32.4889 29 -0.06 0.9525
donorgroup Ins. pos. T1D   -4.6861 22.1941 29 -0.21 0.8343
donorgroup No diabetes   0 . . . .
donorgroup*region Ins. neg. T1D PB -11.1702 50.8142 58 -0.22 0.8268
donorgroup*region Ins. neg. T1D PH -9.6170 49.5998 58 -0.19 0.8469
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 6.3865 34.7127 58 0.18 0.8547
donorgroup*region Ins. pos. T1D PH 34.2323 33.8831 58 1.01 0.3165
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 58 4.96 0.0103
donorgroup 2 29 0.27 0.7642
donorgroup*region 4 58 0.34 0.8494

The SAS System

The PRINT Procedure

Data Set WORK.ALL

Description arh1 cs csh hf un unr vc
-2 Res Log Likelihood 1000.9 997.7 993.7 996.7 984.6 984.6 1005.1
AIC (Smaller is Better) 1008.9 1001.7 1001.7 1004.7 996.6 996.6 1007.1
AICC (Smaller is Better) 1009.4 1001.9 1002.2 1005.2 997.6 997.6 1007.1
BIC (Smaller is Better) 1014.8 1004.7 1007.5 1010.6 1005.4 1005.4 1008.6

The SAS System

The PRINT Procedure

Data Set WORK.STATUS

Obs Reason Status pdG pdH covar
1 Convergence criteria met. 0 1 1 arh(1)
2 Convergence criteria met. 0 1 1 cs
3 Convergence criteria met. 0 1 1 csh
4 Convergence criteria met. 0 1 1 hf
5 Convergence criteria met. 0 1 1 un
6 WARNING: Stopped because of too many likelihood evaluations. 1 1 1 un1
7 Convergence criteria met. 0 1 1 unr
8 Convergence criteria met. 0 1 1 vc
In [149]:
PROC mixed data=duct3 /*maxiter=1000 maxfunc=5000  can also use covtest*/;
     class nPODCaseID donorgroup region;
     model  duct_thickness_absolute =region|donorgroup/solution; /*can use  ddfm = kenwardroger after solution for unbalanced data to improve performance of t and f tests*/
     /*option e3 after solution helps to describe how type 3 tests were constructed*/
     repeated  region/ subject=nPODCaseID(donorgroup)  type=un; 
     lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;
run;
Out[149]:
SAS Output

SAS Output

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.DUCT3
Dependent Variable duct_thickness_absolute
Covariance Structure Unstructured
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 32 6052 6062 6079 6087 6195 6209 6228 6233 6238 6243 6247 6265 6278 6293 6318 6334 6339 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6434 6445 6471 6472
donorgroup 3 Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 6
Columns in X 16
Columns in Z 0
Subjects 32
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 96
Number of Observations Used 96
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 1005.09231733  
1 1 984.57693375 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
UN(1,1) nPODCaseI(donorgrou) 5098.70
UN(2,1) nPODCaseI(donorgrou) 758.47
UN(2,2) nPODCaseI(donorgrou) 6039.81
UN(3,1) nPODCaseI(donorgrou) 2762.97
UN(3,2) nPODCaseI(donorgrou) 928.46
UN(3,3) nPODCaseI(donorgrou) 3398.08

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 984.6
AIC (Smaller is Better) 996.6
AICC (Smaller is Better) 997.6
BIC (Smaller is Better) 1005.4

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
5 20.52 0.0010

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     259.67 14.5733 29 17.82 <.0001
region   PB 56.1677 13.6264 29 4.12 0.0003
region   PH 36.5530 21.7672 29 1.68 0.1038
region   PT 0 . . . .
donorgroup Ins. neg. T1D   -1.9525 32.5868 29 -0.06 0.9526
donorgroup Ins. pos. T1D   -4.6861 22.2610 29 -0.21 0.8347
donorgroup No diabetes   0 . . . .
donorgroup*region Ins. neg. T1D PB -11.1702 30.4695 29 -0.37 0.7166
donorgroup*region Ins. neg. T1D PH -9.6170 48.6729 29 -0.20 0.8447
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 6.3865 20.8146 29 0.31 0.7612
donorgroup*region Ins. pos. T1D PH 34.2323 33.2499 29 1.03 0.3117
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 29 13.38 <.0001
donorgroup 2 29 0.21 0.8109
donorgroup*region 4 29 0.39 0.8143

Least Squares Means

Least Squares Means
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t| Alpha Lower Upper
region   PB 312.03 14.9749 29 20.84 <.0001 0.05 281.40 342.66
region   PH 302.22 16.2985 29 18.54 <.0001 0.05 268.88 335.55
region   PT 257.46 12.2251 29 21.06 <.0001 0.05 232.46 282.46
donorgroup Ins. neg. T1D   281.70 25.5149 29 11.04 <.0001 0.05 229.51 333.88
donorgroup Ins. pos. T1D   299.43 14.7310 29 20.33 <.0001 0.05 269.30 329.56
donorgroup No diabetes   290.58 12.7575 29 22.78 <.0001 0.05 264.49 316.67
donorgroup*region Ins. neg. T1D PB 302.72 35.7026 29 8.48 <.0001 0.05 229.70 375.74
donorgroup*region Ins. neg. T1D PH 284.66 38.8581 29 7.33 <.0001 0.05 205.18 364.13
donorgroup*region Ins. neg. T1D PT 257.72 29.1465 29 8.84 <.0001 0.05 198.11 317.33
donorgroup*region Ins. pos. T1D PB 317.54 20.6129 29 15.40 <.0001 0.05 275.38 359.70
donorgroup*region Ins. pos. T1D PH 325.77 22.4347 29 14.52 <.0001 0.05 279.89 371.66
donorgroup*region Ins. pos. T1D PT 254.99 16.8277 29 15.15 <.0001 0.05 220.57 289.40
donorgroup*region No diabetes PB 315.84 17.8513 29 17.69 <.0001 0.05 279.33 352.35
donorgroup*region No diabetes PH 296.22 19.4291 29 15.25 <.0001 0.05 256.49 335.96
donorgroup*region No diabetes PT 259.67 14.5733 29 17.82 <.0001 0.05 229.87 289.48

Differences of Least Squares Means

Differences of Least Squares Means
Effect donorgroup region _donorgroup region Estimate Standard
Error
DF t Value Pr > |t| Adjustment Adj P Alpha Lower Upper Adj Lower Adj Upper
region   PB   PH 9.8151 20.5711 29 0.48 0.6368 Tukey-Kramer 0.8826 0.05 -32.2576 51.8877 -40.9876 60.6177
region   PB   PT 54.5732 11.4308 29 4.77 <.0001 Tukey-Kramer 0.0001 0.05 31.1946 77.9517 26.3436 82.8027
region   PH   PT 44.7581 18.2599 29 2.45 0.0205 Tukey-Kramer 0.0520 0.05 7.4125 82.1037 -0.3366 89.8529
donorgroup Ins. neg. T1D   Ins. pos. T1D   -17.7352 29.4621 29 -0.60 0.5519 Tukey-Kramer 0.8202 0.05 -77.9919 42.5216 -90.4951 55.0247
donorgroup Ins. neg. T1D   No diabetes   -8.8816 28.5265 29 -0.31 0.7578 Tukey-Kramer 0.9481 0.05 -67.2250 49.4617 -79.3311 61.5678
donorgroup Ins. pos. T1D   No diabetes   8.8535 19.4873 29 0.45 0.6530 Tukey-Kramer 0.8929 0.05 -31.0025 48.7096 -39.2726 56.9797
donorgroup*region Ins. neg. T1D PB Ins. neg. T1D PH 18.0615 49.0448 29 0.37 0.7154 Tukey-Kramer 1.0000 0.05 -82.2464 118.37 -146.04 182.16
donorgroup*region Ins. neg. T1D PB Ins. neg. T1D PT 44.9975 27.2527 29 1.65 0.1095 Tukey-Kramer 0.7694 0.05 -10.7406 100.74 -46.1880 136.18
donorgroup*region Ins. neg. T1D PB Ins. pos. T1D PB -14.8233 41.2258 29 -0.36 0.7218 Tukey-Kramer 1.0000 0.05 -99.1395 69.4930 -152.76 123.11
donorgroup*region Ins. neg. T1D PB Ins. pos. T1D PH -23.0543 42.1663 29 -0.55 0.5887 Tukey-Kramer 0.9997 0.05 -109.29 63.1854 -164.14 118.03
donorgroup*region Ins. neg. T1D PB Ins. pos. T1D PT 47.7310 39.4696 29 1.21 0.2363 Tukey-Kramer 0.9479 0.05 -32.9934 128.46 -84.3310 179.79
donorgroup*region Ins. neg. T1D PB No diabetes PB -13.1228 39.9167 29 -0.33 0.7447 Tukey-Kramer 1.0000 0.05 -94.7617 68.5161 -146.68 120.44
donorgroup*region Ins. neg. T1D PB No diabetes PH 6.4919 40.6468 29 0.16 0.8742 Tukey-Kramer 1.0000 0.05 -76.6402 89.6240 -129.51 142.49
donorgroup*region Ins. neg. T1D PB No diabetes PT 43.0450 38.5624 29 1.12 0.2735 Tukey-Kramer 0.9669 0.05 -35.8239 121.91 -85.9816 172.07
donorgroup*region Ins. neg. T1D PH Ins. neg. T1D PT 26.9360 43.5344 29 0.62 0.5409 Tukey-Kramer 0.9993 0.05 -62.1018 115.97 -118.73 172.60
donorgroup*region Ins. neg. T1D PH Ins. pos. T1D PB -32.8848 43.9869 29 -0.75 0.4607 Tukey-Kramer 0.9975 0.05 -122.85 57.0785 -180.06 114.29
donorgroup*region Ins. neg. T1D PH Ins. pos. T1D PH -41.1158 44.8695 29 -0.92 0.3670 Tukey-Kramer 0.9901 0.05 -132.88 50.6526 -191.25 109.01
donorgroup*region Ins. neg. T1D PH Ins. pos. T1D PT 29.6695 42.3453 29 0.70 0.4891 Tukey-Kramer 0.9984 0.05 -56.9364 116.28 -112.01 171.35
donorgroup*region Ins. neg. T1D PH No diabetes PB -31.1843 42.7624 29 -0.73 0.4717 Tukey-Kramer 0.9979 0.05 -118.64 56.2746 -174.26 111.90
donorgroup*region Ins. neg. T1D PH No diabetes PH -11.5696 43.4447 29 -0.27 0.7919 Tukey-Kramer 1.0000 0.05 -100.42 77.2848 -156.93 133.79
donorgroup*region Ins. neg. T1D PH No diabetes PT 24.9835 41.5010 29 0.60 0.5519 Tukey-Kramer 0.9995 0.05 -59.8956 109.86 -113.88 163.84
donorgroup*region Ins. neg. T1D PT Ins. pos. T1D PB -59.8208 35.6989 29 -1.68 0.1045 Tukey-Kramer 0.7556 0.05 -132.83 13.1917 -179.27 59.6248
donorgroup*region Ins. neg. T1D PT Ins. pos. T1D PH -68.0518 36.7809 29 -1.85 0.0745 Tukey-Kramer 0.6505 0.05 -143.28 7.1737 -191.12 55.0142
donorgroup*region Ins. neg. T1D PT Ins. pos. T1D PT 2.7335 33.6555 29 0.08 0.9358 Tukey-Kramer 1.0000 0.05 -66.0997 71.5667 -109.88 115.34
donorgroup*region Ins. neg. T1D PT No diabetes PB -58.1203 34.1788 29 -1.70 0.0997 Tukey-Kramer 0.7414 0.05 -128.02 11.7831 -172.48 56.2391
donorgroup*region Ins. neg. T1D PT No diabetes PH -38.5056 35.0287 29 -1.10 0.2807 Tukey-Kramer 0.9697 0.05 -110.15 33.1361 -155.71 78.6975
donorgroup*region Ins. neg. T1D PT No diabetes PT -1.9525 32.5868 29 -0.06 0.9526 Tukey-Kramer 1.0000 0.05 -68.6000 64.6949 -110.99 107.08
donorgroup*region Ins. pos. T1D PB Ins. pos. T1D PH -8.2310 28.3160 29 -0.29 0.7734 Tukey-Kramer 1.0000 0.05 -66.1438 49.6818 -102.97 86.5121
donorgroup*region Ins. pos. T1D PB Ins. pos. T1D PT 62.5543 15.7344 29 3.98 0.0004 Tukey-Kramer 0.0110 0.05 30.3739 94.7347 9.9083 115.20
donorgroup*region Ins. pos. T1D PB No diabetes PB 1.7005 27.2683 29 0.06 0.9507 Tukey-Kramer 1.0000 0.05 -54.0695 57.4704 -89.5371 92.9380
donorgroup*region Ins. pos. T1D PB No diabetes PH 21.3152 28.3263 29 0.75 0.4578 Tukey-Kramer 0.9974 0.05 -36.6186 79.2490 -73.4624 116.09
donorgroup*region Ins. pos. T1D PB No diabetes PT 57.8682 25.2442 29 2.29 0.0293 Tukey-Kramer 0.3785 0.05 6.2379 109.50 -26.5970 142.33
donorgroup*region Ins. pos. T1D PH Ins. pos. T1D PT 70.7853 25.1346 29 2.82 0.0086 Tukey-Kramer 0.1537 0.05 19.3793 122.19 -13.3130 154.88
donorgroup*region Ins. pos. T1D PH No diabetes PB 9.9315 28.6703 29 0.35 0.7315 Tukey-Kramer 1.0000 0.05 -48.7059 68.5689 -85.9970 105.86
donorgroup*region Ins. pos. T1D PH No diabetes PH 29.5462 29.6784 29 1.00 0.3277 Tukey-Kramer 0.9833 0.05 -31.1529 90.2453 -69.7552 128.85
donorgroup*region Ins. pos. T1D PH No diabetes PT 66.0992 26.7525 29 2.47 0.0196 Tukey-Kramer 0.2865 0.05 11.3842 120.81 -23.4125 155.61
donorgroup*region Ins. pos. T1D PT No diabetes PB -60.8538 24.5325 29 -2.48 0.0192 Tukey-Kramer 0.2819 0.05 -111.03 -10.6793 -142.94 21.2298
donorgroup*region Ins. pos. T1D PT No diabetes PH -41.2391 25.7033 29 -1.60 0.1195 Tukey-Kramer 0.7948 0.05 -93.8083 11.3301 -127.24 44.7622
donorgroup*region Ins. pos. T1D PT No diabetes PT -4.6861 22.2610 29 -0.21 0.8347 Tukey-Kramer 1.0000 0.05 -50.2150 40.8428 -79.1696 69.7975
donorgroup*region No diabetes PB No diabetes PH 19.6147 24.5224 29 0.80 0.4303 Tukey-Kramer 0.9960 0.05 -30.5392 69.7686 -62.4352 101.66
donorgroup*region No diabetes PB No diabetes PT 56.1677 13.6264 29 4.12 0.0003 Tukey-Kramer 0.0076 0.05 28.2987 84.0368 10.5750 101.76
donorgroup*region No diabetes PH No diabetes PT 36.5530 21.7672 29 1.68 0.1038 Tukey-Kramer 0.7536 0.05 -7.9659 81.0719 -36.2782 109.38
In [150]:
%explore(percent_duct_area);
Out[150]:
SAS Output

SAS Output

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.DUCT3
Dependent Variable percent_duct_area
Covariance Structure Variance Components
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method Parameter
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 32 6052 6062 6079 6087 6195 6209 6228 6233 6238 6243 6247 6265 6278 6293 6318 6334 6339 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6434 6445 6471 6472
donorgroup 3 Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 1
Columns in X 16
Columns in Z 0
Subjects 32
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 96
Number of Observations Used 96
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 101.46823142  
1 1 101.46823142 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
region nPODCaseI(donorgrou) 0.1495

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 101.5
AIC (Smaller is Better) 103.5
AICC (Smaller is Better) 103.5
BIC (Smaller is Better) 104.9

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
0 0.00 1.0000

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     0.3979 0.09665 29 4.12 0.0003
region   PB 0.2562 0.1367 58 1.87 0.0659
region   PH 0.01149 0.1367 58 0.08 0.9333
region   PT 0 . . . .
donorgroup Ins. neg. T1D   0.2793 0.2161 29 1.29 0.2065
donorgroup Ins. pos. T1D   0.2997 0.1476 29 2.03 0.0516
donorgroup No diabetes   0 . . . .
donorgroup*region Ins. neg. T1D PB 0.3137 0.3056 58 1.03 0.3090
donorgroup*region Ins. neg. T1D PH 0.2871 0.3056 58 0.94 0.3514
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 0.1635 0.2088 58 0.78 0.4369
donorgroup*region Ins. pos. T1D PH 0.2470 0.2088 58 1.18 0.2416
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 58 6.58 0.0027
donorgroup 2 29 16.12 <.0001
donorgroup*region 4 58 0.55 0.7000

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.DUCT3
Dependent Variable percent_duct_area
Covariance Structure Compound Symmetry
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method Profile
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 32 6052 6062 6079 6087 6195 6209 6228 6233 6238 6243 6247 6265 6278 6293 6318 6334 6339 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6434 6445 6471 6472
donorgroup 3 Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 2
Columns in X 16
Columns in Z 0
Subjects 32
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 96
Number of Observations Used 96
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 101.46823142  
1 1 100.47420440 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
CS nPODCaseI(donorgrou) 0.01646
Residual   0.1330

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 100.5
AIC (Smaller is Better) 104.5
AICC (Smaller is Better) 104.6
BIC (Smaller is Better) 107.4

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
1 0.99 0.3188

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     0.3979 0.09665 29 4.12 0.0003
region   PB 0.2562 0.1289 58 1.99 0.0516
region   PH 0.01149 0.1289 58 0.09 0.9293
region   PT 0 . . . .
donorgroup Ins. neg. T1D   0.2793 0.2161 29 1.29 0.2065
donorgroup Ins. pos. T1D   0.2997 0.1476 29 2.03 0.0516
donorgroup No diabetes   0 . . . .
donorgroup*region Ins. neg. T1D PB 0.3137 0.2883 58 1.09 0.2811
donorgroup*region Ins. neg. T1D PH 0.2871 0.2883 58 1.00 0.3235
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 0.1635 0.1970 58 0.83 0.4100
donorgroup*region Ins. pos. T1D PH 0.2470 0.1970 58 1.25 0.2148
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 58 7.39 0.0014
donorgroup 2 29 13.21 <.0001
donorgroup*region 4 58 0.62 0.6517

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.DUCT3
Dependent Variable percent_duct_area
Covariance Structure Unstructured
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 32 6052 6062 6079 6087 6195 6209 6228 6233 6238 6243 6247 6265 6278 6293 6318 6334 6339 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6434 6445 6471 6472
donorgroup 3 Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 6
Columns in X 16
Columns in Z 0
Subjects 32
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 96
Number of Observations Used 96
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 101.46823142  
1 1 85.65015667 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
UN(1,1) nPODCaseI(donorgrou) 0.1456
UN(2,1) nPODCaseI(donorgrou) -0.00861
UN(2,2) nPODCaseI(donorgrou) 0.2345
UN(3,1) nPODCaseI(donorgrou) 0.03648
UN(3,2) nPODCaseI(donorgrou) 0.02150
UN(3,3) nPODCaseI(donorgrou) 0.06835

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 85.7
AIC (Smaller is Better) 97.7
AICC (Smaller is Better) 98.7
BIC (Smaller is Better) 106.4

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
5 15.82 0.0074

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     0.3979 0.06536 29 6.09 <.0001
region   PB 0.2562 0.09387 29 2.73 0.0107
region   PH 0.01149 0.1274 29 0.09 0.9288
region   PT 0 . . . .
donorgroup Ins. neg. T1D   0.2793 0.1462 29 1.91 0.0660
donorgroup Ins. pos. T1D   0.2997 0.09984 29 3.00 0.0055
donorgroup No diabetes   0 . . . .
donorgroup*region Ins. neg. T1D PB 0.3137 0.2099 29 1.49 0.1458
donorgroup*region Ins. neg. T1D PH 0.2871 0.2849 29 1.01 0.3220
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 0.1635 0.1434 29 1.14 0.2636
donorgroup*region Ins. pos. T1D PH 0.2470 0.1946 29 1.27 0.2145
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 29 15.39 <.0001
donorgroup 2 29 13.21 <.0001
donorgroup*region 4 29 1.20 0.3334

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.DUCT3
Dependent Variable percent_duct_area
Covariance Structure Unstructured using Correlations
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 32 6052 6062 6079 6087 6195 6209 6228 6233 6238 6243 6247 6265 6278 6293 6318 6334 6339 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6434 6445 6471 6472
donorgroup 3 Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 6
Columns in X 16
Columns in Z 0
Subjects 32
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 96
Number of Observations Used 96
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 101.46823142  
1 1 85.65015667 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 0.1456
Var(2) nPODCaseI(donorgrou) 0.2345
Var(3) nPODCaseI(donorgrou) 0.06835
Corr(2,1) nPODCaseI(donorgrou) -0.04662
Corr(3,1) nPODCaseI(donorgrou) 0.3657
Corr(3,2) nPODCaseI(donorgrou) 0.1698

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 85.7
AIC (Smaller is Better) 97.7
AICC (Smaller is Better) 98.7
BIC (Smaller is Better) 106.4

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
5 15.82 0.0074

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     0.3979 0.06536 29 6.09 <.0001
region   PB 0.2562 0.09387 29 2.73 0.0107
region   PH 0.01149 0.1274 29 0.09 0.9288
region   PT 0 . . . .
donorgroup Ins. neg. T1D   0.2793 0.1462 29 1.91 0.0660
donorgroup Ins. pos. T1D   0.2997 0.09984 29 3.00 0.0055
donorgroup No diabetes   0 . . . .
donorgroup*region Ins. neg. T1D PB 0.3137 0.2099 29 1.49 0.1458
donorgroup*region Ins. neg. T1D PH 0.2871 0.2849 29 1.01 0.3220
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 0.1635 0.1434 29 1.14 0.2636
donorgroup*region Ins. pos. T1D PH 0.2470 0.1946 29 1.27 0.2145
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 29 15.39 <.0001
donorgroup 2 29 13.21 <.0001
donorgroup*region 4 29 1.20 0.3334

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.DUCT3
Dependent Variable percent_duct_area
Covariance Structure Banded
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 32 6052 6062 6079 6087 6195 6209 6228 6233 6238 6243 6247 6265 6278 6293 6318 6334 6339 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6434 6445 6471 6472
donorgroup 3 Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 6
Columns in X 16
Columns in Z 0
Subjects 32
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 96
Number of Observations Used 96
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 2 95.19891028  
1 39 161.13575536 3433.4223981
2 39 161.13575536 3433.4223984
3 39 161.13575536 3433.4223987

Convergence Status

WARNING: Stopped because of too many likelihood evaluations.

Covariance Parameter Values At Last Iteration

Covariance Parameter Values At Last Iteration
Cov Parm Subject Estimate
UN(1,1) nPODCaseI(donorgrou) 0.6920
UN(2,1) nPODCaseI(donorgrou) 0
UN(2,2) nPODCaseI(donorgrou) 0.7997
UN(3,1) nPODCaseI(donorgrou) 0
UN(3,2) nPODCaseI(donorgrou) 0
UN(3,3) nPODCaseI(donorgrou) 0.5000

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.DUCT3
Dependent Variable percent_duct_area
Covariance Structure Heterogeneous Compound Symmetry
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 32 6052 6062 6079 6087 6195 6209 6228 6233 6238 6243 6247 6265 6278 6293 6318 6334 6339 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6434 6445 6471 6472
donorgroup 3 Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 4
Columns in X 16
Columns in Z 0
Subjects 32
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 96
Number of Observations Used 96
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 101.46823142  
1 2 88.91134902 0.00002106
2 1 88.91059679 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 0.1457
Var(2) nPODCaseI(donorgrou) 0.2415
Var(3) nPODCaseI(donorgrou) 0.06637
CSH nPODCaseI(donorgrou) 0.1650

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 88.9
AIC (Smaller is Better) 96.9
AICC (Smaller is Better) 97.4
BIC (Smaller is Better) 102.8

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
3 12.56 0.0057

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     0.3979 0.06440 29 6.18 <.0001
region   PB 0.2562 0.1060 58 2.42 0.0188
region   PH 0.01149 0.1290 58 0.09 0.9293
region   PT 0 . . . .
donorgroup Ins. neg. T1D   0.2793 0.1440 29 1.94 0.0623
donorgroup Ins. pos. T1D   0.2997 0.09838 29 3.05 0.0049
donorgroup No diabetes   0 . . . .
donorgroup*region Ins. neg. T1D PB 0.3137 0.2369 58 1.32 0.1907
donorgroup*region Ins. neg. T1D PH 0.2871 0.2884 58 1.00 0.3236
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 0.1635 0.1618 58 1.01 0.3167
donorgroup*region Ins. pos. T1D PH 0.2470 0.1970 58 1.25 0.2149
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 58 11.03 <.0001
donorgroup 2 29 12.26 0.0001
donorgroup*region 4 58 0.84 0.5072

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.DUCT3
Dependent Variable percent_duct_area
Covariance Structure Huynh-Feldt
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 32 6052 6062 6079 6087 6195 6209 6228 6233 6238 6243 6247 6265 6278 6293 6318 6334 6339 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6434 6445 6471 6472
donorgroup 3 Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 4
Columns in X 16
Columns in Z 0
Subjects 32
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 96
Number of Observations Used 96
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 101.46823142  
1 2 97.00021418 0.01537116
2 1 96.44764550 0.00115071
3 1 96.40885632 0.00001239
4 1 96.40845976 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 0.1847
Var(2) nPODCaseI(donorgrou) 0.1967
Var(3) nPODCaseI(donorgrou) 0.08531
HF nPODCaseI(donorgrou) 0.1330

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 96.4
AIC (Smaller is Better) 104.4
AICC (Smaller is Better) 104.9
BIC (Smaller is Better) 110.3

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
3 5.06 0.1675

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     0.3979 0.07302 29 5.45 <.0001
region   PB 0.2562 0.1289 58 1.99 0.0516
region   PH 0.01149 0.1289 58 0.09 0.9293
region   PT 0 . . . .
donorgroup Ins. neg. T1D   0.2793 0.1633 29 1.71 0.0979
donorgroup Ins. pos. T1D   0.2997 0.1115 29 2.69 0.0118
donorgroup No diabetes   0 . . . .
donorgroup*region Ins. neg. T1D PB 0.3137 0.2883 58 1.09 0.2811
donorgroup*region Ins. neg. T1D PH 0.2871 0.2883 58 1.00 0.3235
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 0.1635 0.1970 58 0.83 0.4100
donorgroup*region Ins. pos. T1D PH 0.2470 0.1970 58 1.25 0.2148
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 58 7.39 0.0014
donorgroup 2 29 12.01 0.0002
donorgroup*region 4 58 0.62 0.6517

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.DUCT3
Dependent Variable percent_duct_area
Covariance Structure Heterogeneous Autoregressive
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 32 6052 6062 6079 6087 6195 6209 6228 6233 6238 6243 6247 6265 6278 6293 6318 6334 6339 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6434 6445 6471 6472
donorgroup 3 Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 4
Columns in X 16
Columns in Z 0
Subjects 32
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 96
Number of Observations Used 96
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 101.46823142  
1 2 90.85121592 0.00000011
2 1 90.85121206 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
Var(1) nPODCaseI(donorgrou) 0.1466
Var(2) nPODCaseI(donorgrou) 0.2345
Var(3) nPODCaseI(donorgrou) 0.06790
ARH(1) nPODCaseI(donorgrou) 0.06196

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 90.9
AIC (Smaller is Better) 98.9
AICC (Smaller is Better) 99.3
BIC (Smaller is Better) 104.7

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
3 10.62 0.0140

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     0.3979 0.06514 29 6.11 <.0001
region   PB 0.2562 0.1156 58 2.22 0.0306
region   PH 0.01149 0.1339 58 0.09 0.9319
region   PT 0 . . . .
donorgroup Ins. neg. T1D   0.2793 0.1457 29 1.92 0.0651
donorgroup Ins. pos. T1D   0.2997 0.09951 29 3.01 0.0053
donorgroup No diabetes   0 . . . .
donorgroup*region Ins. neg. T1D PB 0.3137 0.2584 58 1.21 0.2297
donorgroup*region Ins. neg. T1D PH 0.2871 0.2993 58 0.96 0.3414
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 0.1635 0.1765 58 0.93 0.3583
donorgroup*region Ins. pos. T1D PH 0.2470 0.2045 58 1.21 0.2319
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 58 9.29 0.0003
donorgroup 2 29 14.80 <.0001
donorgroup*region 4 58 0.73 0.5735

The SAS System

The PRINT Procedure

Data Set WORK.ALL

Description arh1 cs csh hf un unr vc
-2 Res Log Likelihood 90.9 100.5 88.9 96.4 85.7 85.7 101.5
AIC (Smaller is Better) 98.9 104.5 96.9 104.4 97.7 97.7 103.5
AICC (Smaller is Better) 99.3 104.6 97.4 104.9 98.7 98.7 103.5
BIC (Smaller is Better) 104.7 107.4 102.8 110.3 106.4 106.4 104.9

The SAS System

The PRINT Procedure

Data Set WORK.STATUS

Obs Reason Status pdG pdH covar
1 Convergence criteria met. 0 1 1 arh(1)
2 Convergence criteria met. 0 1 1 cs
3 Convergence criteria met. 0 1 1 csh
4 Convergence criteria met. 0 1 1 hf
5 Convergence criteria met. 0 1 1 un
6 WARNING: Stopped because of too many likelihood evaluations. 1 1 1 un1
7 Convergence criteria met. 0 1 1 unr
8 Convergence criteria met. 0 1 1 vc
In [151]:
PROC mixed data=duct3 /*maxiter=1000 maxfunc=5000  can also use covtest*/;
     class nPODCaseID donorgroup region;
     model  duct_area =region|donorgroup/solution; /*can use  ddfm = kenwardroger after solution for unbalanced data to improve performance of t and f tests*/
     /*option e3 after solution helps to describe how type 3 tests were constructed*/
     repeated  region/ subject=nPODCaseID(donorgroup)  type=un; 
     lsmeans region|donorgroup/adjust=tukey cl pdiff alpha=0.05;
run;
Out[151]:
SAS Output

SAS Output

The SAS System

The Mixed Procedure

The MIXED Procedure

Model Information

Model Information
Data Set WORK.DUCT3
Dependent Variable duct_area
Covariance Structure Unstructured
Subject Effect nPODCaseI(donorgrou)
Estimation Method REML
Residual Variance Method None
Fixed Effects SE Method Model-Based
Degrees of Freedom Method Between-Within

Class Level Information

Class Level Information
Class Levels Values
nPODCaseID 32 6052 6062 6079 6087 6195 6209 6228 6233 6238 6243 6247 6265 6278 6293 6318 6334 6339 6353 6357 6360 6362 6371 6380 6382 6385 6396 6416 6417 6434 6445 6471 6472
donorgroup 3 Ins. neg. T1D Ins. pos. T1D No diabetes
region 3 PB PH PT

Dimensions

Dimensions
Covariance Parameters 6
Columns in X 16
Columns in Z 0
Subjects 32
Max Obs per Subject 3

Number of Observations

Number of Observations
Number of Observations Read 96
Number of Observations Used 96
Number of Observations Not Used 0

Iteration History

Iteration History
Iteration Evaluations -2 Res Log Like Criterion
0 1 161.73567993  
1 1 146.41832438 0.00000000

Convergence Status

Convergence criteria met.

Covariance Parameter Estimates

Covariance Parameter Estimates
Cov Parm Subject Estimate
UN(1,1) nPODCaseI(donorgrou) 0.3446
UN(2,1) nPODCaseI(donorgrou) -0.01386
UN(2,2) nPODCaseI(donorgrou) 0.3785
UN(3,1) nPODCaseI(donorgrou) 0.1345
UN(3,2) nPODCaseI(donorgrou) -0.00976
UN(3,3) nPODCaseI(donorgrou) 0.1733

Fit Statistics

Fit Statistics
-2 Res Log Likelihood 146.4
AIC (Smaller is Better) 158.4
AICC (Smaller is Better) 159.5
BIC (Smaller is Better) 167.2

Null Model Likelihood Ratio Test

Null Model Likelihood Ratio Test
DF Chi-Square Pr > ChiSq
5 15.32 0.0091

Solution for Fixed Effects

Solution for Fixed Effects
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t|
Intercept     0.8757 0.1041 29 8.41 <.0001
region   PB 0.4936 0.1248 29 3.96 0.0005
region   PH 0.2769 0.1890 29 1.47 0.1535
region   PT 0 . . . .
donorgroup Ins. neg. T1D   -0.07779 0.2327 29 -0.33 0.7406
donorgroup Ins. pos. T1D   0.01107 0.1590 29 0.07 0.9450
donorgroup No diabetes   0 . . . .
donorgroup*region Ins. neg. T1D PB -0.06619 0.2790 29 -0.24 0.8141
donorgroup*region Ins. neg. T1D PH -0.00525 0.4225 29 -0.01 0.9902
donorgroup*region Ins. neg. T1D PT 0 . . . .
donorgroup*region Ins. pos. T1D PB 0.01725 0.1906 29 0.09 0.9285
donorgroup*region Ins. pos. T1D PH 0.1800 0.2886 29 0.62 0.5378
donorgroup*region Ins. pos. T1D PT 0 . . . .
donorgroup*region No diabetes PB 0 . . . .
donorgroup*region No diabetes PH 0 . . . .
donorgroup*region No diabetes PT 0 . . . .

Type 3 Tests of Fixed Effects

Type 3 Tests of Fixed Effects
Effect Num DF Den DF F Value Pr > F
region 2 29 11.85 0.0002
donorgroup 2 29 0.42 0.6625
donorgroup*region 4 29 0.12 0.9725

Least Squares Means

Least Squares Means
Effect donorgroup region Estimate Standard
Error
DF t Value Pr > |t| Alpha Lower Upper
region   PB 1.3307 0.1231 29 10.81 <.0001 0.05 1.0789 1.5825
region   PH 1.1887 0.1290 29 9.21 <.0001 0.05 0.9248 1.4525
region   PT 0.8535 0.08730 29 9.78 <.0001 0.05 0.6749 1.0320
donorgroup Ins. neg. T1D   1.0310 0.1762 29 5.85 <.0001 0.05 0.6705 1.3914
donorgroup Ins. pos. T1D   1.2094 0.1017 29 11.89 <.0001 0.05 1.0013 1.4175
donorgroup No diabetes   1.1326 0.08812 29 12.85 <.0001 0.05 0.9523 1.3128
donorgroup*region Ins. neg. T1D PB 1.2253 0.2935 29 4.17 0.0002 0.05 0.6250 1.8256
donorgroup*region Ins. neg. T1D PH 1.0696 0.3076 29 3.48 0.0016 0.05 0.4405 1.6988
donorgroup*region Ins. neg. T1D PT 0.7979 0.2081 29 3.83 0.0006 0.05 0.3722 1.2236
donorgroup*region Ins. pos. T1D PB 1.3976 0.1695 29 8.25 <.0001 0.05 1.0510 1.7442
donorgroup*region Ins. pos. T1D PH 1.3437 0.1776 29 7.57 <.0001 0.05 0.9805 1.7069
donorgroup*region Ins. pos. T1D PT 0.8868 0.1202 29 7.38 <.0001 0.05 0.6410 1.1326
donorgroup*region No diabetes PB 1.3693 0.1468 29 9.33 <.0001 0.05 1.0691 1.6694
donorgroup*region No diabetes PH 1.1527 0.1538 29 7.49 <.0001 0.05 0.8381 1.4672
donorgroup*region No diabetes PT 0.8757 0.1041 29 8.41 <.0001 0.05 0.6629 1.0886

Differences of Least Squares Means

Differences of Least Squares Means
Effect donorgroup region _donorgroup region Estimate Standard
Error
DF t Value Pr > |t| Adjustment Adj P Alpha Lower Upper Adj Lower Adj Upper
region   PB   PH 0.1421 0.1817 29 0.78 0.4407 Tukey-Kramer 0.7170 0.05 -0.2296 0.5137 -0.3067 0.5908
region   PB   PT 0.4772 0.1046 29 4.56 <.0001 Tukey-Kramer 0.0002 0.05 0.2632 0.6913 0.2188 0.7357
region   PH   PT 0.3352 0.1585 29 2.11 0.0432 Tukey-Kramer 0.1044 0.05 0.01097 0.6594 -0.05630 0.7267
donorgroup Ins. neg. T1D   Ins. pos. T1D   -0.1784 0.2035 29 -0.88 0.3878 Tukey-Kramer 0.6590 0.05 -0.5946 0.2378 -0.6810 0.3242
donorgroup Ins. neg. T1D   No diabetes   -0.1016 0.1970 29 -0.52 0.6100 Tukey-Kramer 0.8644 0.05 -0.5046 0.3014 -0.5882 0.3850
donorgroup Ins. pos. T1D   No diabetes   0.07681 0.1346 29 0.57 0.5726 Tukey-Kramer 0.8367 0.05 -0.1985 0.3521 -0.2556 0.4092
donorgroup*region Ins. neg. T1D PB Ins. neg. T1D PH 0.1557 0.4333 29 0.36 0.7220 Tukey-Kramer 1.0000 0.05 -0.7304 1.0418 -1.2940 1.6053
donorgroup*region Ins. neg. T1D PB Ins. neg. T1D PT 0.4274 0.2495 29 1.71 0.0974 Tukey-Kramer 0.7342 0.05 -0.08292 0.9377 -0.4074 1.2622
donorgroup*region Ins. neg. T1D PB Ins. pos. T1D PB -0.1723 0.3389 29 -0.51 0.6151 Tukey-Kramer 0.9998 0.05 -0.8655 0.5209 -1.3063 0.9617
donorgroup*region Ins. neg. T1D PB Ins. pos. T1D PH -0.1184 0.3431 29 -0.35 0.7325 Tukey-Kramer 1.0000 0.05 -0.8201 0.5833 -1.2663 1.0295
donorgroup*region Ins. neg. T1D PB Ins. pos. T1D PT 0.3385 0.3172 29 1.07 0.2947 Tukey-Kramer 0.9746 0.05 -0.3102 0.9872 -0.7227 1.3997
donorgroup*region Ins. neg. T1D PB No diabetes PB -0.1440 0.3282 29 -0.44 0.6641 Tukey-Kramer 0.9999 0.05 -0.8152 0.5272 -1.2420 0.9541
donorgroup*region Ins. neg. T1D PB No diabetes PH 0.07264 0.3314 29 0.22 0.8280 Tukey-Kramer 1.0000 0.05 -0.6051 0.7504 -1.0361 1.1814
donorgroup*region Ins. neg. T1D PB No diabetes PT 0.3496 0.3114 29 1.12 0.2709 Tukey-Kramer 0.9658 0.05 -0.2874 0.9865 -0.6924 1.3916
donorgroup*region Ins. neg. T1D PH Ins. neg. T1D PT 0.2717 0.3779 29 0.72 0.4780 Tukey-Kramer 0.9981 0.05 -0.5013 1.0446 -0.9928 1.5362
donorgroup*region Ins. neg. T1D PH Ins. pos. T1D PB -0.3280 0.3512 29 -0.93 0.3581 Tukey-Kramer 0.9889 0.05 -1.0463 0.3903 -1.5031 0.8471
donorgroup*region Ins. neg. T1D PH Ins. pos. T1D PH -0.2741 0.3552 29 -0.77 0.4466 Tukey-Kramer 0.9969 0.05 -1.0006 0.4524 -1.4626 0.9144
donorgroup*region Ins. neg. T1D PH Ins. pos. T1D PT 0.1828 0.3303 29 0.55 0.5841 Tukey-Kramer 0.9997 0.05 -0.4926 0.8583 -0.9222 1.2878
donorgroup*region Ins. neg. T1D PH No diabetes PB -0.2997 0.3408 29 -0.88 0.3865 Tukey-Kramer 0.9925 0.05 -0.9967 0.3974 -1.4400 0.8407
donorgroup*region Ins. neg. T1D PH No diabetes PH -0.08304 0.3439 29 -0.24 0.8109 Tukey-Kramer 1.0000 0.05 -0.7864 0.6204 -1.2338 1.0677
donorgroup*region Ins. neg. T1D PH No diabetes PT 0.1939 0.3247 29 0.60 0.5551 Tukey-Kramer 0.9995 0.05 -0.4703 0.8581 -0.8927 1.2805
donorgroup*region Ins. neg. T1D PT Ins. pos. T1D PB -0.5997 0.2684 29 -2.23 0.0333 Tukey-Kramer 0.4116 0.05 -1.1486 -0.05070 -1.4977 0.2984
donorgroup*region Ins. neg. T1D PT Ins. pos. T1D PH -0.5458 0.2736 29 -1.99 0.0556 Tukey-Kramer 0.5588 0.05 -1.1054 0.01385 -1.4613 0.3697
donorgroup*region Ins. neg. T1D PT Ins. pos. T1D PT -0.08886 0.2403 29 -0.37 0.7143 Tukey-Kramer 1.0000 0.05 -0.5804 0.4027 -0.8930 0.7153
donorgroup*region Ins. neg. T1D PT No diabetes PB -0.5713 0.2547 29 -2.24 0.0327 Tukey-Kramer 0.4063 0.05 -1.0922 -0.05045 -1.4235 0.2808
donorgroup*region Ins. neg. T1D PT No diabetes PH -0.3547 0.2588 29 -1.37 0.1810 Tukey-Kramer 0.8998 0.05 -0.8840 0.1746 -1.2207 0.5112
donorgroup*region Ins. neg. T1D PT No diabetes PT -0.07779 0.2327 29 -0.33 0.7406 Tukey-Kramer 1.0000 0.05 -0.5537 0.3982 -0.8564 0.7009
donorgroup*region Ins. pos. T1D PB Ins. pos. T1D PH 0.05389 0.2501 29 0.22 0.8309 Tukey-Kramer 1.0000 0.05 -0.4577 0.5655 -0.7831 0.8909
donorgroup*region Ins. pos. T1D PB Ins. pos. T1D PT 0.5108 0.1440 29 3.55 0.0014 Tukey-Kramer 0.0314 0.05 0.2162 0.8054 0.02882 0.9928
donorgroup*region Ins. pos. T1D PB No diabetes PB 0.02832 0.2242 29 0.13 0.9004 Tukey-Kramer 1.0000 0.05 -0.4302 0.4868 -0.7218 0.7784
donorgroup*region Ins. pos. T1D PB No diabetes PH 0.2449 0.2289 29 1.07 0.2933 Tukey-Kramer 0.9741 0.05 -0.2231 0.7130 -0.5208 1.0107
donorgroup*region Ins. pos. T1D PB No diabetes PT 0.5219 0.1989 29 2.62 0.0137 Tukey-Kramer 0.2200 0.05 0.1151 0.9286 -0.1435 1.1873
donorgroup*region Ins. pos. T1D PH Ins. pos. T1D PT 0.4569 0.2182 29 2.09 0.0451 Tukey-Kramer 0.4962 0.05 0.01064 0.9032 -0.2732 1.1870
donorgroup*region Ins. pos. T1D PH No diabetes PB -0.02558 0.2304 29 -0.11 0.9124 Tukey-Kramer 1.0000 0.05 -0.4968 0.4456 -0.7965 0.7453
donorgroup*region Ins. pos. T1D PH No diabetes PH 0.1910 0.2349 29 0.81 0.4228 Tukey-Kramer 0.9955 0.05 -0.2895 0.6716 -0.5951 0.9771
donorgroup*region Ins. pos. T1D PH No diabetes PT 0.4680 0.2058 29 2.27 0.0306 Tukey-Kramer 0.3891 0.05 0.04697 0.8890 -0.2208 1.1567
donorgroup*region Ins. pos. T1D PT No diabetes PB -0.4825 0.1897 29 -2.54 0.0166 Tukey-Kramer 0.2534 0.05 -0.8704 -0.09453 -1.1172 0.1522
donorgroup*region Ins. pos. T1D PT No diabetes PH -0.2659 0.1952 29 -1.36 0.1837 Tukey-Kramer 0.9028 0.05 -0.6651 0.1333 -0.9190 0.3872
donorgroup*region Ins. pos. T1D PT No diabetes PT 0.01107 0.1590 29 0.07 0.9450 Tukey-Kramer 1.0000 0.05 -0.3141 0.3362 -0.5208 0.5430
donorgroup*region No diabetes PB No diabetes PH 0.2166 0.2166 29 1.00 0.3256 Tukey-Kramer 0.9829 0.05 -0.2264 0.6597 -0.5082 0.9414
donorgroup*region No diabetes PB No diabetes PT 0.4936 0.1248 29 3.96 0.0005 Tukey-Kramer 0.0115 0.05 0.2384 0.7487 0.07615 0.9110
donorgroup*region No diabetes PH No diabetes PT 0.2769 0.1890 29 1.47 0.1535 Tukey-Kramer 0.8619 0.05 -0.1095 0.6634 -0.3553 0.9092